Genes and uses for plant enhancement

ABSTRACT

The present invention discloses transgenic seeds for crops with enhanced agronomic traits are provided by trait-improving recombinant DNA in the nucleus of cells of the seed where plants grown from such transgenic seed exhibit one or more enhanced traits as compared to a control plant. Of particular interest are transgenic plants that have increased yield. The present invention also provides recombinant DNA molecules for expression of a protein, and recombinant DNA molecules for suppression of a protein.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a divisional of U.S. application Ser. No. 13/999,850, filed Mar. 27, 2014, which application is a continuation of U.S. application Ser. No. 13/140,920, filed Jun. 21, 2011, which is a national stage application under 35 U.S.C. §371 of PCT/US2009/068351, filed Dec. 17, 2009, and published as WO 2010/075143 on Jul. 1, 2010, which claims the benefit of priority to U.S. provisional application Ser. No. 61/203,529, filed Dec. 22, 2008, which applications and publication are incorporated by reference as if reproduced herein and made a part hereof in their entirety, and the benefit of priority of each of which is claimed herein, along with sequence listings and computer program listings.

INCORPORATION OF SEQUENCE LISTING

This document incorporates by reference herein an electronic sequence listing text file, which is filed in electronic format via EFS-Web with the application. The text file is named “1598740.txt,” is 17,264,640 bytes, and was created on Jul. 12, 2016.

FIELD OF THE INVENTION

Disclosed herein are transgenic plant cells, plants and seeds comprising recombinant DNA and methods of making and using such plant cells, plants and seeds.

SUMMARY OF THE INVENTION

This invention provides plant cell nuclei with recombinant DNA that imparts enhanced agronomic traits in transgenic plants having the nuclei in their cells, e.g. enhanced water use efficiency, enhanced cold tolerance, enhanced heat tolerance, enhanced shade tolerance, enhanced high salinity tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein or enhanced seed oil. In certain cases the trait is imparted by producing in the cells a protein that is encoded by recombinant DNA and/or in other cases the trait is imparted by suppressing the production of a protein that is natively produced in the cells.

Such recombinant DNA in a plant cell nucleus of this invention is provided in as a construct comprising a promoter that is functional in plant cells and that is operably linked to DNA that encodes a protein or to DNA that results in gene suppression. Such DNA in the construct is sometimes defined by protein domains of an encoded protein targeted for production or suppression, e.g. a “Pfam domain module” (as defined herein below) from the group of Pfam domain modules identified in Table 17. Alternatively, e.g. where a Pfam domain module is not available, such DNA in the construct is defined a consensus amino acid sequence of an encoded protein that is targeted for production or suppression, e.g. a protein having amino acid sequence with at least 90%, with at least 95%, with at least 98%, and with at least 99%, or 99.5% identity to a consensus amino acid sequence in the group of SEQ ID NO: 6027 through SEQ ID NO: 6034, or their corresponding nucleic acid sequences.

Other aspects of the invention are directed to specific derivative physical forms of the transgenic plant cell nuclei, e.g. where such a transgenic nucleus is present in a transgenic plant cell, a transgenic plant including plant part(s) such as progeny transgenic seed, and a haploid reproductive derivative of plant cell such as Iransgenic pollen and transgenic ovule. Such plant cell nuclei and derivatives are advantageously selected from a population of transgenic plants regenerated from plant cells having a nucleus that is transformed with recombinant DNA by screening the transgenic plants or progeny seeds in the population for an enhanced trait as compared to control plants or seed that do not have the recombinant DNA in their nuclei, where the enhanced trait is enhanced water use efficiency, enhanced cold tolerance, enhanced heat tolerance, enhanced shade tolerance, enhanced high salinity tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein or enhanced seed oil.

One aspect of the present invention includes a plant cell nucleus with stably integrated, recombinant DNA, wherein said recombinant DNA comprises a promoter that is functional in said plant cell and that is operably linked to a protein coding DNA encoding a protein having an amino acid sequence comprising a Pfam domain module selected from the group consisting of WRKY::WRKY, AP2, AUX_IAA, WRKY, WRKY, HLH, Myb_DNA-binding::Linker_histone, zf-B_box::zf-B_box, Ank::Ank::Ank::Chromo, NAM, zf-C2H2, Myb_DNA-binding, bZIP_1, PHD, Linker_histone::AT_hook::AT_hook::AT_hook::AT_hook, B3::Auxin_resp, HLH, zf-Dof, AT_hook::DUF296, AT_hook::AT_hook::DUF296, NAM, GATA, NAM, Myb_DNA-binding, zf-B_box::CCT, POX::Homeobox, B3::Auxin_resp::AUX_IAA, Myb_DNA-binding::Myb_DNA-binding, Myb_DNA-binding::Myb_DNA-binding, zf-C2H2, zf-C2H2, Myb_DNA-binding::Myb_DNA-binding, Myb_DNA-binding::Myb_DNA-binding, TCP, KNOX1::KNOX2, zf-ZPR1::zf-ZPR1, Myb_DNA-binding::Myb_DNA-binding, DUF630::DUF632, WRKY, Myb_DNA-binding, zf-C2H2, HLH, AP2, AT_hook::DUF296, Ank::Ank::Ank::Ank::Ank, WRKY, zf-C2H2, NAM, AP2, NAM, Myb_DNA-binding::Myb_DNA-binding::Myb_DNA-binding, NAM, HLH, Myb_DNA-binding::Myb_DNA-binding, Myb_DNA-binding, HLH, bZIP_2, bZIP_2, BAH::PHD, HLH, NAM, GATA, SSrccog::Rtt106::HMG_box, DUF573, zf-B_box::CCT, HLH, RWP-RK, AP2::B3, AUX_IAA, SRF-TF, AP2, AP2, HSF_DNA-bind, AP2, SRF-TF::K-box, Myb_DNA-binding, zf-LSD1::zf-LSD1::zf-LSD1, KNOX1::KNOX2::ELK, zf-C3HC4, MFMR::bZIP_1, DUF573, Myb_DNA-binding, HLH, NAM, Myb_DNA-binding::Myb_DNA-binding, SRF-TF::K-box, zf-C3HC4, zf-B_box, WRKY, zf-B_box::CCT, EIN3, HSF_DNA-bind, AUX_IAA, TCP, Myb_DNA-binding::Myb_DNA-binding, AP2, KNOX1::KNOX2::ELK::IHomeobox, HSF_DNA-bind, HSF_DNA-bind, AP2::B3, NAM, SBP, AP2, zf-C2H2. SRF-TF::K-box, zf-C2H2, GRAS, AP2, Myb_DNA-binding, AP2, AP2::AP2, HLH, CXC::CXC, AP2, NAM, zf-C3HC4, Myb_DNA-binding::Myb_DNA-binding, GRAS, Homeobox::HALZ, Myb_DNA-binding, NAM, WRKY, zf-C2H2, zf-C2H2, NAM, zf-C2H2, AP2::AP2, ef-C3HC4, RWP-RK::PB1, SRF-TF::K-box, and zf-B_box; said recombinant DNA comprises a promoter that is functional in said plant cell and that is operably linked to a protein coding DNA encoding a protein comprising an amino acid sequence with at least 90% identity to a consensus amino acid sequence selected from the group consisting of SEQ ID NO: 6027 through 6034; or said recombinant DNA suppresses comprises a promoter that is functional in said plant cell and operably linked to DNA that transcribe into RNA that suppresses the level of an endogenous protein wherein said endogenous protein has an amino acid sequence comprising a pfam domain module selected from the group consisting of RWP-RK, AUX_IAA, SRF-TF, zf-C3HC4, Myb_DNA-binding, CCT, PHD, EIN3, and AP2; and wherein said plant cell nucleus is selected by screening a population of transgenic plants that have said recombinant DNA and an enhanced trait as compared to control plants that do not have said recombinant DNA in their nuclei; and wherein said enhanced trait is selected from group of enhanced traits consisting of enhanced water use efficiency, enhanced cold tolerance, enhanced heat tolerance, enhanced resistance to salt exposure, enhanced shade tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.

In another aspect of the present invention, the plant cell nucleus where said protein coding DNA encodes a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 140 through SEQ ID NO: 6023. In addition, the plant cell nucleus can comprising DNA expressing a protein that provides tolerance from exposure to an herbicide, e.g, glyphosate, dicamba, or glufosinate, applied at levels that are lethal to a wild type of said plant cell.

Yet in another aspect of the invention includes a plurality of plant cells or planys with the plant cell nucleus described, and the transgenic plant cell or plant are homozygous for said recombinant DNA. In addition, these plant cells are transgenic seeds from crops such as a corn, soybean, cotton, canola, alfalfa, wheat or rice plant, or transgenic pollen grain comprising a haploid derivative of a plant cell nucleus.

One aspect of the present invention includes a method for manufacturing non-natural, transgenic seed that can be used to produce a crop of transgenic plants with an enhanced trait resulting from expression of recombinant DNA in a nucleus described, wherein said method for manufacturing said transgenic seed comprising (a) screening a population of plants for said enhanced trait and said recombinant DNA, wherein individual plants in said population can exhibit said trait at a level less than, essentially the same as or greater than the level that said trait is exhibited in control plants which do not contain the recombinant DNA, wherein said enhanced trait is selected from the group of enhanced traits consisting of enhanced water use eticiency, enhanced cold tolerance, enhanced heat tolerance, enhanced high salinity tolerance, enhanced shade tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil, (b) selecting from said population one or more plants that exhibit said trait at a level greater than the level that said trait is exhibited in control plants, and (c) collecting seeds from selected plant selected from step b.

In another aspect, the method for manufacturing transgenic seed, e.g, corn, soybean, cotton, alfalfa, canola wheat or rice seed, further comprising (a) verifying that said recombinant DNA is stably integrated in said selected plants, and (b) analyzing tissue of said selected plant to determine the expression or suppression of a protein having the function of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 140-278.

Yet another aspect of the present invention includes a method of producing hybrid corn seed comprising (a) acquiring hybrid corn seed from a herbicide tolerant corn plant which also has stably-integrated, recombinant DNA in a nucleus of claim 2: (b) producing corn plants from said hybrid corn seed, wherein a fraction of the plants produced from said hybrid corn seed is homozygous for said recombinant DNA, a fraction of the plants produced from said hybrid corn seed is hemizygous for said recombinant DNA, and a fraction of the plants produced from said hybrid corn seed has none of said recombinant DNA; (c) selecting corn plants which are homozygous and hemizygous for said recombinant DNA by treating with an herbicide; (d) collecting seed from herbicide-treated-surviving corn plants and planting said seed to produce further progeny corn plants; (e) repeating steps (c) and (d) at least once to produce an inbred corn line; and (f) crossing said inbred corn line with a second corn line to produce hybrid seed.

In one aspect of the invention, the transgenic plant comprise recombinant DNA constructs for expressing proteins arc characterized by amino acid sequence that have at least 90% identity over at least 90% of the length of a reference sequence selected from the group consisting of SEQ ID NOs: 140-278 when the amino acid sequence is aligned to the reference sequence.

In one aspect of the invention, the transgenic plant comprise recombinant DNA constructs for expressing proteins are characterized by amino acid sequence that have at least 92.5% identity over at least 92.5% of the length of a reference sequence selected from the group consisting of SEQ ID NOs: 140-278 when the amino acid sequence is aligned to the reference sequence.

In one aspect of the invention, the transgenic plant comprise recombinant DNA constructs for expressing proteins are characterized by amino acid sequence that have at least 95% identity over at least 95% of the length of a reference sequence selected from the group consisting of SEQ ID NOs: 140-278 when the amino acid sequence is aligned to the reference sequence.

In one aspect of the invention, the transgenic plant comprise recombinant DNA constructs for expressing proteins are characterized by amino acid sequence that have at least 97% identity over at least 97% of the length of a reference sequence selected from the group consisting of SEQ ID NOs: 140-278 when the amino acid sequence is aligned to the reference sequence.

In one aspect of the invention, the transgenic plant comprise recombinant DNA constructs for expressing proteins are characterized by amino acid sequence that have at least 98% identity over at least 98% of the length of a reference sequence selected from the group consisting of SEQ ID NOs: 140-278 when the amino acid sequence is aligned to the reference sequence.

In one aspect of the invention, the transgenic plant comprise recombinant DNA constructs for expressing proteins are characterized by amino acid sequence that have at least 99% identity over at least 99% of the length of a reference sequence selected from the group consisting of SEQ ID NOs: 140-278 when the amino acid sequence is aligned to the reference sequence.

In one aspect of the invention, the transgenic plant comprise recombinant DNA constructs for expressing proteins are characterized by amino acid sequence that have at least 99.5% identity over at least 99.5% of the length of a reference sequence selected from the group consisting of SEQ ID NOs: 140-278 when the amino acid sequence is aligned to the reference sequence.

In other aspects of the invention the nuclei of plant cells and derivative transgenic cells, plants, seeds, pollen and ovules further include recombinant DNA expressing a protein that provides tolerance from exposure to one or more herbicide applied at levels that are lethal to a wild type plant. Such herbicide tolerance is not only an advantageous trait in such plants but is also useful as a selectable marker in the transformation methods for producing the nuclei and nuclei derivatives of the invention. Such herbicide tolerance includes tolerance to a glyphosate, dicamba, or glufosinate herbicide.

Yet other aspects of the invention provide transgenic plant cell nuclei which are homozygous for the recombinant DNA. The transgenic plant cell nuclei of the invention and dervitave cells, plants, seed and haploid reproductive derivatives of the invention are advantageously provided in corn, soybean, cotton, canola, alfalfa, wheat, rice plants, or combinations thereof.

This invention also provides methods for manufacturing non-natural, transgenic seed that can be used to produce a crop of transgenic plants with an enhanced trait resulting from expression of stably-integrated, recombinant DNA in the nucleus of the plant cells. More specifically the method includes, but are not limited to, (a) screening a population of plants for an enhanced trait and recombinant DNA, where individual plants in the population can exhibit the trait at a level less than, essentially the same as or greater than the level that the trait is exhibited in control plants which do not express the recombinant DNA; (b) selecting from the population one or more plants that exhibit the trait at a level greater than the level that said trait is exhibited in control plants and (c) collecting seed from a selected plant. Such method can further include the steps of (a) verifying that the recombinant DNA is stably integrated in said selected plants; and (b) analyzing tissue of a selected plant to determine the production of a protein having the function of a protein encoded by a recombinant DNA with a sequence of one of SEQ ID NO: 1-139; In one aspect of the invention the plants in the population can further include DNA expressing a protein that provides tolerance to exposure to an herbicide applied at levels that are lethal to wild type plant cells and where the selecting is effected by treating the population with the herbicide, e.g. a glyphosate, dicamba, or glufosinate compound. In another aspect of the invention, the plants are selected by identifying plants with the enhanced trait. The methods can be used for manufacturing corn, soybean, cotton, canola, alfalfa, wheat and/or rice seed selected as having one of the enhanced traits described above.

Another aspect of the invention provides a method of producing hybrid corn seed including the step of acquiring hybrid corn seed from a herbicide tolerant corn plant which also has a nucleus of this invention with stably-integrated, recombinant DNA. The method can further include the steps of producing corn plants from said hybrid corn seed, whenre a fraction of the plants produced from said hybrid corn seed is homozygous for said recombinant DNA, a fraction of the plants produced from said hybrid corn seed is hemizygous for said recombinant DNA, and/or a fraction of the plants produced from said hybrid corn seed has none of said recombinant DNA; selecting corn plants which are homozygous and hemizygous for said recombinant DNA by treating with an herbicide; collecting seed from herbicide-treated-surviving corn plants and planting said seed to produce further progeny corn plants; repeating the selecting and collecting steps at least once to produce an inbred corn line; and crossing the inbred corn line with a second corn line to produce hybrid seed.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1, 2 and 3 are pictures illustrating plasmid maps; and

FIGS. 4(a) and 4(b) illustrate a consensus amino acid sequence of SEQ ID NO: 237 and their homologs.

DETAILED DESCRIPTION OF THE INVENTION

In the attached sequence listing:

SEQ ID NO: 1-139 are nucleotide sequences of the coding strand of DNA for “genes” used in the recombinant DNA imparting an enhanced trait in plant cells, i.e. each represents a coding sequence for a protein;

SEQ ID NO: 140-278 are amino acid sequences of the protein of the “genes” encoding by nucleotide sequence 1-139;

SEQ ID NO: 279-6023 homologs are amino acid sequences of homologous proteins;

SEQ ID NO: 6024 is a nucleotide sequence of a plasmid base vector useful for corn transformation;

SEQ ID NO: 6025 is a DNA sequence of a plasmid base vector useful for soybean transformation;

SEQ ID NO: 6026 is a DNA sequence of a plasmid base vector useful for cotton transformation; and

SEQ ID NO: 6027-6034 are consensus sequences.

Table 1 lists the protein SEQ ID NOs and their corresponding consensus SEQ ID NOs.

TABLE 1 NUC PEP CONSENSUS SEQ ID NO SEQ ID NO GENE ID SEQ ID NO 4 143 CGPG2053 6027 21 160 CGPG2704 6028 23 162 CGPG2735 6029 50 189 CGPG3347 6030 52 191 CGPG3449 6031 95 234 CGPG4537 6032 98 237 CGPG4632 6033 139 278 CGPG8726 6034

The nuclei of this invention are identified by screening transgenic plants for one or more traits including enhanced drought stress tolerance, enhanced heat stress tolerance, enhanced cold stress tolerance, enhanced high salinity stress tolerance, enhanced low nitrogen availability stress tolerance, enhanced shade stress tolerance, enhanced plant growth and development at the stages of seed imbibition through early vegetative phase, and enhanced plant growth and development at the stages of leaf development, flower production and seed maturity.

“Gene” means a chromosomal element for expressing a protein and specifaccly includes the DNA encoding a protein. In cases where expression of a target protein is desired, the pertinent part of a gene is the DNA encoding the target protein; in cases where suppression of a target is desired, the pertinent part of a gene is that part that is transcribed as mRNA. “Recombinant DNA” means a polynucleotide having a genetically engineered modification introduced through combination of endogenous and/or exogenous elements in a transcription unit. Recombinant DNA can include DNA segments obtained from different sources, or DNA segments obtained from the same source, but which have been manipulated to join DNA segments which do not naturally exist in the joined form.

“Trait” means a physiological, morphological, biochemical, or physical characteristic of a plant or particular plant material or cell, or any combinations thereor.

A “control plant” is a plant without trait-improving recombinant DNA in its nucleus. A control plant is used to measure and compare trait enhancement in a transgenic plant with such trait-improving recombinant DNA. A suitable control plant can be a non-transgenic plant of the parental line used to generate a transgenic plant herein. Alternatively, a control plant can be a transgenic plant having an empty vector or marker gene, but does not contain the recombinant DNA that produces the trait enhancement. A control plant can also be a negative segregant progeny of hemizygous transgenic plant. In certain demonstrations of trait enhancement, the use of a limited number of control plants can cause a wide variation in the control dataset. To minimize the effect of the variation within the control dataset, a “reference” is used. As use herein a “reference” is a trimmed mean of all data from both transgenic and control plants grown under the same conditions and at the same developmental stage. The trimmed mean is calculated by eliminating a specific percentage, e.g., 20%, of the smallest and largest observation from the data set and then calculating the average of the remaining observation.

“Trait enhancement” means a detectable and desirable difference in a characteristic in a transgenic plant relative to a control plant or a reference. In some cases, the trait enhancement can be measured quantitatively. For example, the trait enhancement can entail at least a 2% desirable difference in an observed trait, at least a 5% desirable difference, at least about a 10% desirable difference, at least about a 20% desirable difference, at least about a 30% desirable difference, at least about a 50% desirable difference, at least about a 70% desirable difference, at least about a 80% desirable difference, at least about a 90% desirable difference, at least about a 92.5% desirable difference, at least about a 95% desirable difference, at least about a 98% desirable difference, at least about a 99% desirable difference, at least about a 99.5% desirable difference or at least about a 100% difference, or an even greater desirable difference. In other cases, the trait enhancement is only measured qualitatively. It is known that there can be a natural variation in a trait. Therefore, the trait enhancement observed entails a change of the normal distribution of the trait in the transgenic plant compared with the trait distribution observed in a control plant or a reference, which is evaluated by statistical methods provided herein. Trait enhancement includes, but is not limited to, yield increase, including increased yield under non-stress conditions and increased yield under environmental stress conditions. Stress conditions can include, for example, drought, shade, fungal disease, viral disease, bacterial disease, insect infestation, nematode infestation, cold temperature exposure, heat exposure, osmotic stress, reduced nitrogen nutrient availability, reduced phosphorus nutrient availability, high plant density, or any combinations thereof.

Many agronomic traits can affect “yield”, including without limitation, plant height, pod number, pod position on the plant, number of internodes, incidence of pod shatter, grain size, efficiency of nodulation and nitrogen fixation, efficiency of nutrient assimilation, resistance to biotic and abiotic stress, carbon assimilation, plant architecture, resistance to lodging, percent seed germination, seedling vigor, juvenile traits, or any combinations thereof. Other traits that can affect yield include, efficiency of germination (including germination in stressed conditions), growth rate (including growth rate in stressed conditions), ear number, seed number per ear, seed size, composition of seed (starch, oil, protein) and characteristics of seed fill. Also of interest is the generation of transgenic plants that demonstrate desirable phenotypic properties that can confer an increase in overall plant yield. Such properties include enhanced plant morphology, plant physiology or improved components of the mature seed harvested from the transgenic plant.

“Yield-limiting environment” means the condition under which a plant would have the limitation on yield including environmental stress conditions.

“Stress condition” means a condition unfavorable for a plant, which adversely affect plant metabolism, growth and/or development. A plant under the stress condition typically shows reduced germination rate, retarded growth and development, reduced photosynthesis rate, and eventually leading to reduction in yield. Specifically, “water deficit stress” used herein refers to the sub-optimal conditions for water and humidity needed for normal growth of natural plants. Relative water content (RWC) can be used as a physiological measure of plant water deficit. It measures the effect of osmotic adjustment in plant water status, when a plant is under stressed conditions. Conditions which can result in water deficit stress include, but are not limited to, heat, drought, high salinity and PEG induced osmotic stress.

“Cold stress” means the exposure of a plant to a temperatures below (two or more degrees Celsius below) those normal for a particular species or particular strain of plant.

“Nitrogen nutrient” means any one or any mix of the nitrate salts commonly used as plant nitrogen fertilizer, including, but not limited to, potassium nitrate, calcium nitrate, sodium nitrate, ammonium nitrate. The term ammonium as used herein means any one or any mix of the ammonium salts commonly used as plant nitrogen fertilizer, e.g., ammonium nitrate, ammonium chloride, ammonium sulfate, etc.

“Low nitrogen availability stress” means a plant growth condition that does not contain sufficient nitrogen nutrient to maintain a healthy plant growth and/or for a plant to reach its typical yield under a sufficient nitrogen growth condition. For example, a limiting nitrogen condition can refers to a growth condition with 50% or less of the conventional nitrogen inputs. “Sufficient nitrogen growth condition” means a growth condition where the soil or growth medium contains or receives optimal amounts of nitrogen nutrient to sustain a healthy plant growth and/or for a plant to reach its typical yield for a particular plant species or a particular strain. One skilled in the art would recognize what constitute such soil, media and fertilizer inputs for most plant species.

“Shade stress” means a growth condition that has limited light availability that triggers the shade avoidance response in plant. Plants are subject to shade stress when localized at lower part of the canopy, or in close proximity of neighboring vegetation. Shade stress can become exacerbated when the planting density exceeds the average prevailing density for a particular plant species.

“Increased yield” of a transgenic plant of the present invention is evidenced and measured in a number of ways, including test weight, seed number per plant, seed weight, seed number per unit area (e.g., seeds, or weight of seeds, per acre), bushels per acre, tons per acre, tons per acre, kilo per hectare. For example, maize yield can be measured as production of shelled corn kernels per unit of production area, e.g., in bushels per acre or metric tons per hectare, often reported on a moisture adjusted basis, e.g., at 15.5% moisture. Increased yield can result from enhanced utilization of key biochemical compounds, such as nitrogen, phosphorous and carbohydrate, or from enhanced tolerance to environmental stresses, such as cold, heat, drought, salt, and attack by pests or pathogens. Trait-improving recombinant DNA can also be used to provide transgenic plants having enhanced growth and development, and ultimately increased yield, as the result of modified expression of plant growth regulators or modification of cell cycle or photosynthesis pathways.

A “plant promoter” is a promoter capable of initiating transcription in plant cells whether or not its origin is a plant cell. Exemplary plant promoters include, but are not limited to, those that are obtained from plants, plant viruses, and bacteria which include genes expressed in plant cells such Agrobacterium or Rhizobium. Examples of promoters under developmental control include promoters that preferentially initiate transcription in certain tissues, such as leaves, roots, or seeds. Such promoters are referred to as “tissue preferred”. Promoters which initiate transcription only in certain tissues are referred to as “tissue specific”. A “cell type” specific promoter primarily drives expression in certain cell types in one or more organs, for example, vascular cells in roots or leaves. An “inducible” or “repressible” promoter is a promoter which is under environmental control. Examples of environmental conditions that can effect transcription by inducible promoters include anaerobic conditions, or certain chemicals, or the presence of light. Tissue specific, tissue preferred, cell type specific, and inducible promoters constitute the class of “non-constitutive” promoters. A “constitutive” promoter is a promoter which is active under most conditions.

As used herein, “operably linked” refers to the association of two or more nucleic acid elements in a recombinant DNA construct, e.g. as when a promoter is operably linked with DNA that is transcribed to RNA whether for expressing or suppressing a protein. Recombinant DNA constructs can be designed to express a protein which can be an endogenous protein, an exogenous homologue of an endogenous protein or an exogenous protein with no native homologue. Alternatively, recombinant DNA constructs can be designed to suppress the level of an endogenous protein, e.g. by suppression of the native gene. Such gene suppression can be effectively employed through a native RNA interference (RNAi) mechanism in which recombinant DNA comprises both sense and anti-sense oriented DNA matched to the gene targeted for suppression where the recombinant DNA is transcribed into RNA that can form a double-strand to initiate an RNAi mechanism. Gene suppression can also be effected by recombinant DNA that comprises anti-sense oriented DNA matched to the gene targeted for suppression. Gene suppression can also be effected by recombinant DNA that comprises DNA that is transcribed to a microRNA matched to the gene targeted for suppression. In the examples illustrating the invention recombinant DNA for effecting gene suppression that imparts is identified by the term “antisense”. It will be understood by a person of ordinary skill in the art that any of the ways of effecting gene suppression are contemplated and enabled by a showing of one approach to gene suppression.

A “consensus amino acid sequence” means an artificial, amino acid sequence indicating conserved amino acids in the sequence of homologous proteins as determined by statistical analysis of an optimal alignment, e.g. CLUSTALW, of amino acid sequence of homolog proteins. The consensus sequences listed in the sequence listing were created by identifying the most frequent amino acid at each position in a set of aligned protein sequences. When there was 100% identity in an alignment the amino acid is indicated by a capital letter. When the occurrence of an amino acid is at least about 70% in an alignment, the amino acid is indicated by a lower case letter. When there is no amino acid occurrence of at least about 70%, e.g. due to diversity or gaps, the amino acid is indicated by an “x”. When used to defined embodiments of the invention, a consensus amino acid sequence will be aligned with a query protein amino acid sequence in an optimal alignment, e.g. CLUSTALW. An embodiment of the invention will have identity to the conserved amino acids indicated in the consensus amino acid sequence.

As used herein a “homolog” means a protein in a group of proteins that perform the same biological function, e.g. proteins that belong to the same Pfam protein family and that provide a common enhanced trait in transgenic plants of this invention. Homologs are expressed by homologous genes. With reference to homologous genes, homologs include orthologs, e.g. genes expressed in different species that evolved from a common ancestral genes by speciation and encode proteins retain the same function, but do not include paralogs, e.g., genes that are related by duplication but have evolved to encode proteins with different functions. Homologous genes include naturally occurring alleles and artificially-created variants. Degeneracy of the genetic code provides the possibility to substitute at least one base of the protein encoding sequence of a gene with a different base without causing the amino acid sequence of the polypeptide produced from the gene to be changed. When optimally aligned, homolog proteins have typically at least about 60% identity, in some instances at least about 70%, for example about 80% and even at least about 90% identity over the full length of a protein, such as from SEQ ID No. 140-278, identified as being associated with imparting an enhanced trait when expressed in plant cells. In one aspect of the invention homolog proteins have an amino acid sequence that has at least 95%, 98%, 99%, or 99.5% identity to a consensus amino acid sequence of proteins and homologs disclosed herein.

Homologs are identified by comparison of amino acid sequence, e.g. manually or by use of a computer-based tool using known homology-based search algorithms such as those commonly known and referred to as BLAST, FASTA, and Smith-Waterman. A local sequence alignment program, e.g. BLAST, can be used to search a database of sequences to find similar sequences, and the summary Expectation value (E-value) used to measure the sequence base similarity. Because a protein hit with the best E-value for a particular organism may not necessarily be an ortholog, i.e. have the same function, or be the only ortholog, a reciprocal query is used to filter hit sequences with significant E-values for ortholog identification. The reciprocal query entails search of the significant hits against a database of amino acid sequences from the base organism that are similar to the sequence of the query protein. A hit can be identified as an ortholog, when the reciprocal query's best hit is the query protein itself or a protein encoded by a duplicated gene after speciation. A further aspect of the homologs encoded by DNA useful in the transgenic plants of the invention are those proteins that differ from a disclosed protein as the result of deletion or insertion of one or more amino acids in a native sequence.

As used herein, “percent identity” means the extent to which two optimally aligned DNA or protein segments are invariant throughout a window of alignment of components, for example nucleotide sequence or amino acid sequence. An “identity fraction” for aligned segments of a test sequence and a reference sequence is the number of identical components that are shared by sequences of the two aligned segments divided by the total number of sequence components in the reference segment over a window of alignment which is the smaller of the full test sequence or the full reference sequence. “Percent identity” (“% identity”) is the identity fraction times 100. Such optimal alignment is understood to be deemed as local alignment of DNA sequences. For protein alignment, a local alignment of protein sequences should allow introduction of gaps to achieve optimal alignment. Percent identity is calculated over the aligned length not including the gaps introduced by the alignment per se.

Homologous genes are genes which encode proteins with the same or similar biological function to the protein encoded by the second gene. Homologous genes can be generated by the event of speciation (see ortholog) or by the event of genetic duplication (see paralog). “Orthologs” refer to a set of homologous genes in different species that evolved from a common ancestral gene by specification. Normally, orthologs retain the same function in the course of evolution; and “paralogs” refer to a set of homologous genes in the same species that have diverged from each other as a consequence of genetic duplication. Thus, homologous genes can be from the same or a different organism. As used herein, “homolog” means a protein that performs the same biological function as a second protein including those identified by sequence identity search.

“Arabidopsis” means plants of Arabidopsis thaliana.

“Pfam” database is a large collection of multiple sequence alignments and hidden Markov models covering many common protein families, e.g. Pfam version 19.0 (December 2005) contains alignments and models for 8183 protein families and is based on the Swissprot 47.0 and SP-TrEMBL 30.0 protein sequence databases. See S. R. Eddy, “Profile Hidden Markov Models”, Bioinformatics 14:755-763, 1998. The Pfam database is currently maintained and updated by the Pfam Consortium. The alignments represent some evolutionary conserved structure that has implications for the protein's function. Profile hidden Markov models (profile HMMs) built from the protein family alignments are useful for automatically recognizing that a new protein belongs to an existing protein family even if the homology by alignment appears to be low.

A “Pfam domain module” is a representation of Pfam domains in a protein, in order from N terminus to C terminus. In a Pfam domain module individual Pfam domains are separated by double colons “::”. The order and copy number of the Pfam domains from N to C terminus are attributes of a Pfam domain module. Although the copy number of repetitive domains is important, varying copy number often enables a similar function. Thus, a Pfam domain module with multiple copies of a domain should define an equivalent Pfam domain module with variance in the number of multiple copies. A Pfam domain module is not specific for distance between adjacent domains, but contemplates natural distances and variations in distance that provide equivalent function. The Pfam database contains both narrowly- and broadly-defined domains, leading to identification of overlapping domains on some proteins. A Pfam domain module is characterized by non-overlapping domains. Where there is overlap, the domain having a function that is more closely associated with the function of the protein (based on the E value of the Pfam match) is selected.

Once one DNA is identified as encoding a protein which imparts an enhanced trait when expressed in transgenic plants, other DNA encoding proteins with the same Pfam domain module are identified by querying the amino acid sequence of protein encoded by candidate DNA against the Hidden Markov Models which characterizes the Pfam domains using HMMER software, a current version of which is provided in the appended computer listing. Candidate proteins meeting the same Pfam domain module are in the protein family and have corresponding DNA that is useful in constructing recombinant DNA for the use in the plant cells of this invention. Hidden Markov Model databases for use with HMMER software in identifying DNA expressing protein with a common Pfam domain module for recombinant DNA in the plant cells of this invention are also included in the appended computer listing.

Version 19.0 of the IIMMER software and Pfam databases were used to identify known domains in the proteins corresponding to amino acid sequence of SEQ ID NO: 140 through SEQ ID NO:278. All DNA encoding proteins that have scores higher than the gathering cutoff disclosed in Table 19 by Pfam analysis disclosed herein can be used in recombinant DNA of the plant cells of this invention, e.g. for selecting transgenic plants having enhanced agronomic traits. The relevant Pfam modules for use in this invention, as more specifically disclosed below, are WRKY::WRKY, AP2, AUX_IAA, WRKY, WRKY, HLH, Myb_DNA-binding::Linker_histone, zf-B_box::zf-B_box, Ank::Ank::Ank::Chromo, NAM, zf-C2H2, Myb_DNA-binding, bZIP_1, PHD, Linker_histone::AT_hook::AT_hook::AT_hook::AT_hook, B3::Auxin_resp, HLH, zf-Dof, AT_hook::DUF296, AT_hook::AT_hook::DUF296, NAM, GATA, NAM, Myb_DNA-binding, zf-B_box::CCT, POX::Homeobox, B3::Auxin_resp::AUX_IAA, Myb_DNA-binding::Myb_DNA-binding, Myb_DNA-binding::Myb_DNA-binding, zf-C2H2, zf-C2H2, Myb_DNA-binding::Myb_DNA-binding, Myb_DNA-binding::Myb_DNA-binding, TCP, KNOX1::KNOX2, zf-ZPR1::zf-ZPR1, Myb_DNA-binding::Myb_DNA-binding, DUF630::DUF632, WRKY, Myb_DNA-binding, zf-C2H2, HLH, AP2, AT_hook::DUF296, Ank::Ank::Ank::Ank::Ank, WRKY, zf-C2H2, NAM, AP2, NAM, Myb_DNA-binding::Myb_DNA-binding::Myb_DNA-binding, NAM, HLH, Myb_DNA-binding::Myb_DNA-binding, Myb_DNA-binding, HLH, bZIP_2, bZIP_2, BAH::PHD, HLH, NAM, GATA, SSrecog::Rtt106::HMG_box, DUF573, zf-B_box::CCT, HLH, RWP-RK, AP2::B3, AUX_IAA, SRF-TF, AP2, AP2, HSF_DNA-bind, AP2, SRF-TF::K-box, Myb_DNA-binding, zf-LSD1::zf-LSD1::zf-LSD1, KNOX1::KNOX2::ELK, zf-C3HC4, MFMR::bZIP_1, DUF573, Myb_DNA-binding, HLH, NAM, Myb_DNA-binding::Myb_DNA-binding, SRF-TF::K-box, zf-C3HC4, zf-B_box, WRKY, zf-B_box::CCT, EIN3, HSF_DNA-bind, AUX_IAA, TCP, Myb_DNA-binding::Myb_DNA-binding, AP2, KNOX1::KNOX2::ELK::Homeobox, HSF_DNA-bind, HSF_DNA-bind, AP2::B3, NAM, SBP, AP2, zf-C2H2, SRF-TF::K-box, zf-C2H2, GRAS, AP2, Myb_DNA-binding, AP2, AP2::AP2, HLH, CXC::CXC, AP2, NAM, zf-C3HC4, Myb_DNA-binding::Myb_DNA-binding, GRAS, Homcobox::HALZ, Myb_DNA-binding, NAM, WRKY, zf-C2H2, zf-C2H2, NAM, zf-C2H2, AP2::AP2, zf-C3HC4, RWP-RK::PB1, SRF-TF::K-box, and zf-B_box.

Recombinant DNA Constructs

The invention uses recombinant DNA for imparting one or more enhanced traits to transgenic plant when incorporated into the nucleus of the plant cells. Such recombinant DNA is a construct comprising a promoter operatively linked to to DNA for expression or suppression of a target protein in plant cells. Other construct components can include additional regulatory elements, such as 5′ or 3′ untranslated regions (such as polyadenylation sites), intron regions, and transit or signal peptides. Such recombinant DNA constructs can be assembled using methods known to those of ordinary skill in the art.

Recombinant constructs prepared in accordance with the present invention also generally include a 3′ untranslated DNA region (UTR) that typically contains a polyadenylation sequence following the polynucleotide coding region. Examples of useful 3′ UTRs include those from the nopaline synthase gene of Agrobacterium tumefaciens (nos), a gene encoding the small subunit of a ribulose-1,5-bisphosphate carboxylase-oxygenase (rbcS), and the T7 transcript of Agrobacterium tumefaciens.

Constructs and vectors can also include a transit peptide for targeting of a gene target to a plant organelle, particularly to a chloroplast, leucoplast or other plastid organelle. For descriptions of the use of chloroplast transit peptides, see U.S. Pat. No. 5,188,642 and U.S. Pat. No. 5,728,925, incorporated herein by reference.

Table 2 provides a list of genes that provided recombinant DNA that was expressed in a model plant and identified from screening as imparting an enhanced trait. When the stated orientation is “sense”, the expression of the gene or a homolog in a crop plant provides the means to identify transgenic events that provide an enhanced trait in the crop plant. When the stated orientation is “antisense”, the suppression of the native homolog in a crop plant provides the means to identify transgenic events that provide an enhanced trait in the crop plant. In some cases the expression/suppression in the model plant exhibited an enhanced trait that corresponds to an enhanced agronomic trait, e.g. cold stress tolerance, water deficit stress tolerance, low nitrogen stress tolerance and the like. In other cases the expression/suppression in the model plant exhibited an enhanced trait that is a surrogate to an enhanced agronomic trait, e.g. salinity stress tolerance being a surrogate to drought tolerance or improvement in plant growth and development being a surrogate to enhanced yield. Even when expression of a transgene or suppression of a native gene imparts an enhanced trait in a model plant, not every crop plant expressing the same transgene or suppressing the same native gene will necessarily demonstrate an indicated enhanced agronomic trait. For instance, it is well known that multiple transgenic events are required to identify a transgenic plant that can exhibit an enhanced agronomic trait. A skilled artisan can identify a transgenic plant cell nuclei, cell, plant or seed by making number of transgenic events, typically a very large number, and engaging in screening processes identified in this specification and illustrated in the examples. For example, a screening process includes selecting only those transgenic events with an intact, single copy of the recombinant DNA in a single locus of the host plant genome and further screening for transgenic events that impart a desired trait that is replicatable when the recombinant DNA is introgressed into a variety of germplams without imparting significant adverse traits.

An understanding of Table 2 is facilitated by the following description of the headings:

“NUC SEQ ID NO” refers to a SEQ ID NO. for particular DNA sequence in the Sequence Listing.

“PEP SEQ ID NO” refers to a SEQ ID NO. in the Sequence Listing for the amino acid sequence of a protein corresponding to a particular DNA

“construct_id” refers to an arbitrary number used to identify a particular recombinant DNA construct comprising the particular DNA.

“Gene ID” refers to an arbitrary name used to identify the particular DNA.

“orientation” refers to the orientation of the particular DNA in a recombinant DNA construct relative to the promoter.

TABLE 2 NUC SEQ PEP ID SEQ ID Construct NO Gene id NO id Orientation 1 CGPG113 140 12796 SENSE 2 CGPG1754 141 18301 SENSE 3 CGPG1809 142 70733 ANTI- SENSE 4 CGPG2053 143 17013 SENSE 5 CGPG2164 144 15707 ANTI- SENSE 6 CGPG2551 145 17507 SENSE 7 CGPG2578 146 17518 SENSE 8 CGPG2583 147 17521 SENSE 9 CGPG2586 148 17523 SENSE 10 CGPG2593 149 17629 SENSE 11 CGPG2594 150 70734 SENSE 12 CGPG26 151 10106 ANTI- SENSE 13 CGPG2604 152 72053 SENSE 14 CGPG2615 153 76106 SENSE 15 CGPG2639 154 17491 SENSE 16 CGPG2644 155 19152 SENSE 17 CGPG2657 156 17907 SENSE 18 CGPG2664 157 17526 SENSE 19 CGPG2678 158 70736 SENSE 20 CGPG2699 159 76073 SENSE 21 CGPG2704 160 76239 SENSE 22 CGPG2711 161 18215 SENSE 23 CGPG2735 162 72674 SENSE 24 CGPG2752 163 17909 SENSE 25 CGPG2757 164 17911 SENSE 26 CGPG2767 165 17914 SENSE 27 CGPG2778 166 74311 SENSE 28 CGPG2797 167 78468 SENSE 29 CGPG2805 168 19640 SENSE 30 CGPG2811 169 71530 SENSE 31 CGPG2907 170 17832 SENSE 32 CGPG2935 171 18504 SENSE 33 CGPG2943 172 18547 SENSE 34 CGPG2948 173 18548 SENSE 35 CGPG2961 174 18387 SENSE 36 CGPG2975 175 18542 SENSE 37 CGPG2985 176 74056 SENSE 38 CGPG3107 177 73821 SENSE 39 CGPG3169 178 18549 SENSE 40 CGPG3171 179 18517 SENSE 41 CGPG3175 180 19644 SENSE 42 CGPG3287 181 18836 SENSE 43 CGPG3289 182 18240 SENSE 44 CGPG3296 183 71309 SENSE 45 CGPG3298 184 19184 SENSE 46 CGPG3309 185 19186 SENSE 47 CGPG3312 186 70336 SENSE 48 CGPG3327 187 18325 SENSE 49 CGPG3341 188 18333 SENSE 50 CGPG3347 189 18248 SENSE 51 CGPG3369 190 18843 SENSE 52 CGPG3449 191 77332 SENSE 53 CGPG3451 192 19650 SENSE 54 CGPG3463 193 18436 SENSE 55 CGPG3468 194 19634 SENSE 56 CGPG3476 195 18509 SENSE 57 CGPG3505 196 18610 SENSE 58 CGPG359 197 10456 ANTI- SENSE 59 CGPG367 198 11115 ANTI- SENSE 60 CGPG3750 199 70449 SENSE 61 CGPG3761 200 70461 SENSE 62 CGPG3793 201 70470 SENSE 63 CGPG3795 202 70452 SENSE 64 CGPG3804 203 70473 SENSE 65 CGPG3810 204 70455 SENSE 66 CGPG3813 205 70542 SENSE 67 CGPG382 206 10362 ANTI- SENSE 68 CGPG3825 207 70479 SENSE 69 CGPG3828 208 70546 SENSE 70 CGPG3837 209 70481 SENSE 71 CGPG3841 210 78318 SENSE 72 CGPG3843 211 72907 SENSE 73 CGPG3857 212 70485 SENSE 74 CGPG3858 213 70486 SENSE 75 CGPG3865 214 70483 SENSE 76 CGPG3868 215 70625 SENSE 77 CGPG3869 216 70489 SENSE 78 CGPG3875 217 74202 SENSE 79 CGPG3879 218 71971 SENSE 80 CGPG3947 219 19880 SENSE 81 CGPG3987 220 19972 SENSE 82 CGPG4004 221 19920 SENSE 83 CGPG4013 222 19995 SENSE 84 CGPG4015 223 19896 SENSE 85 CGPG4061 224 19957 SENSE 86 CGPG4066 225 19826 SENSE 87 CGPG4082 226 19748 SENSE 88 CGPG4106 227 70930 SENSE 89 CGPG4112 228 70983 SENSE 90 CGPG4133 229 19796 SENSE 91 CGPG4166 230 19869 SENSE 92 CGPG4195 231 19924 SENSE 93 CGPG4525 232 71822 SENSE 94 CGPG4527 233 70758 SENSE 95 CGPG4537 234 70760 SENSE 96 CGPG4591 235 75032 SENSE 97 CGPG4612 236 72943 SENSE 98 CGPG4632 237 70773 SENSE 99 CGPG490 238 70215 SENSE 100 CGPG5130 239 73675 SENSE 101 CGPG5278 240 72057 SENSE 102 CGPG5280 241 72093 SENSE 103 CGPG5292 242 72047 SENSE 104 CGPG5306 243 72106 SENSE 105 CGPG5316 244 72117 SENSE 106 CGPG5324 245 72118 SENSE 107 CGPG5330 246 72109 SENSE 108 CGPG5334 247 72129 SENSE 109 CGPG5422 248 74307 SENSE 110 CGPG5599 249 72926 SENSE 111 CGPG690 250 12179 ANTI- SENSE 112 CGPG7354 251 74844 SENSE 113 CGPG7367 252 74810 SENSE 114 CGPG7369 253 74834 SENSE 115 CGPG7373 254 74882 SENSE 116 CGPG7374 255 74894 SENSE 117 CGPG7376 256 74823 SENSE 118 CGPG7378 257 77801 SENSE 119 CGPG7641 258 75494 SENSE 120 CGPG7655 259 75472 SENSE 121 CGPG7678 260 75574 SENSE 122 CGPG7697 261 75517 SENSE 123 CGPG7709 262 75566 SENSE 124 CGPG7714 263 75531 SENSE 125 CGPG7743 264 75594 SENSE 126 CGPG7748 265 75559 SENSE 127 CGPG7757 266 75572 SENSE 128 CGPG7759 267 75596 SENSE 129 CGPG7822 268 75680 SENSE 130 CGPG7840 269 75611 SENSE 131 CGPG7876 270 75751 SENSE 132 CGPG858 271 73934 SENSE 133 CGPG2562 272 74555 SENSE 134 CGPG31 273 10114 ANTI- SENSE 135 CGPG4213 274 78654 SENSE 136 CGPG477 275 10804 ANTI- SENSE 137 CGPG6312 276 77507 SENSE 138 CGPG7188 277 78989 SENSE 139 CGPG8726 278 78560 SENSE

Recombinant DNA

DNA for use in the present invention to improve traits in plants have a nucleotide sequence of SEQ ID NO:1 through SEQ ID NO: 139, as well as the homologs of such DNA molecules. A subset of the DNA for gene suppression aspects of the invention includes fragments of the disclosed full polynucleotides consisting of oligonucleotides of 21 or more consecutive nucleotides. Oligonucleotides the larger molecules having a sequence selected from the group consisting of SEQ ID NO: I through SEQ ID NO: 139 are useful as probes and primers for detection of the polynucleotides used in the invention. Also useful in this invention arc variants of the DNA. Such variants can be naturally occurring, including DNA from homologous genes from the same or a different species, or can be non-natural variants, for example DNA synthesized using chemical synthesis methods, or generated using recombinant DNA techniques. Degeneracy of the genetic code provides the possibility to substitute at least one base of the protein encoding sequence of a gene with a different base without causing the amino acid sequence of the polypeptide produced from the gene to be changed. Hence, a DNA useful in the present invention can have any base sequence that has been changed from the sequences provided herein by substitution in accordance with degeneracy of the genetic code.

Homologs of the genes providing DNA demonstrated as useful in improving traits in model plants disclosed herein will generally have significant identity with the DNA disclosed herein. DNA is substantially identical to a reference DNA if, when the sequences of the polynucleotides are optimally aligned there is at least about 60% nucleotide equivalence over a comparison window. The DNA can also be about 70% equivalence, about 80% equivalence; about 85% equivalence; about 90%; about 95%; or even about 98%, 98.5%, 99% or 99.5% equivalence over a comparison window. A comparison window is at least about 50-100 nucleotides, and/or is the entire length of the polynucleotide provided herein. Optimal alignment of sequences for aligning a comparison window can be conducted by algorithms or by computerized implementations of these algorithms (for example, the Wisconsin Genetics Software Package Release 7.0-10.0, Genetics Computer Group, 575 Science Dr., Madison, Wis.). The reference polynucleotide can be a full-length molecule or a portion of a longer molecule. In one embodiment, the window of comparison for determining polynucleotide identity of protein encoding sequences is the entire coding region.

Proteins useful for imparting enhanced traits are entire proteins or at least a sufficient portion of the entire protein to impart the relevant biological activity of the protein. Proteins used for generation of transgenic plants having enhanced traits include the proteins with an amino acid sequence provided herein as SEQ ID NO: 140 through SEQ ID NO: 278, as well as homologs of such proteins.

Homologs of the trait-improving proteins provided herein generally demonstrate significant sequence identity. Of particular interest are proteins having at least about 50% sequence identity, at least about 70% sequence identity or higher, e.g., at least about 80% sequence identity with an amino acid sequence of SEQ ID NO:140 through SEQ ID NO: 278. Proteins also include those with higher identity, e.g., at least about 100% to at least about 99.5%, at least about 100% to at least about 99%, at least about 100% to at least about 98%, at least about 100% to at least about 97.5%, at least about 100% to at least about 95%, at least about 100% to at least about 92.5%, and at least about 100% to at least about 90%. Identity of protein homologs is determined by aligning the amino acid sequence of a putative protein homolog with a defined amino acid sequence and by calculating the percentage of identical and conservatively substituted amino acids over the window of comparison. The window of comparison for determining identity can be the entire amino acid sequence disclosed herein, e.g., the full sequence of any of SEQ ID NO: 140 through SEQ ID NO: 278.

The relationship of homologs with amino acid sequences of SEQ ID NO: 279 to SEQ ID NO: 6023 to the proteins with amino acid sequences of SEQ ID NO: to 140 to SEQ ID NO: 278 are found in the listing of Table 16.

Other functional homolog proteins differ in one or more amino acids from those of a trait-improving protein disclosed herein as the result of one or more of the well-known conservative amino acid substitutions, e.g., valine is a conservative substitute for alanine and threonine is a conservative substitute for serine. Conservative substitutions for an amino acid within the native sequence can be selected from other members of a class to which the naturally occurring amino acid belongs. Representative amino acids within these various classes include, but are not limited to: (1) acidic (negatively charged) amino acids such as aspartic acid and glutamic acid; (2) basic (positively charged) amino acids such as arginine, histidine, and lysine; (3) neutral polar amino acids such as glycine, serine, threonine, cysteine, tyrosine, asparagine, and glutamine; and (4) neutral nonpolar (hydrophobic) amino acids such as alanine, leucine, isoleucine, valine, proline, phenylalanine, tryptophan, and methionine. Conserved substitutes for an amino acid within a native amino acid sequence can be selected from other members of the group to which the naturally occurring amino acid belongs. For example, a group of amino acids having aliphatic side chains is glycine, alanine, valine, leucine, and isoleucine; a group of amino acids having aliphatic-hydroxyl side chains is serine and threonine; a group of amino acids having amide-containing side chains is asparagine and glutamine; a group of amino acids having aromatic side chains is phenylalanine, tyrosine, and tryptophan; a group of amino acids having basic side chains is lysine, arginine, and histidine; and a group of amino acids having sulfur-containing side chains is cysteine and methionine. Naturally conservative amino acids substitution groups are: valine-leucine, valine-isoleucine, phenylalanine-tyrosine, lysine-arginine, alanine-valine, aspartic acid-glutamic acid, and asparagine-glutamine. A further aspect of the invention includes proteins that differ in one or more amino acids from those of a described protein sequence as the result of deletion or insertion of one or more amino acids in a native sequence.

Genes that are homologous to each other can be grouped into families and included in multiple sequence alignments. Then a consensus sequence for each group can be derived. This analysis enables the derivation of conserved and class-(family) specific residues or motifs that are functionally important. These conserved residues and motifs can be further validated with 3D protein structure if available. The consensus sequence can be used to define the full scope of the invention, e.g., to identify proteins with a homolog relationship. Thus, the present invention contemplates that protein homologs include proteins with an amino acid sequence that has at least 90% identity to such a consensus amino acid sequence sequences.

Promoters

Numerous promoters that are active in plant cells have been described in the literature. These include promoters present in plant genomes as well as promoters from other sources, including nopaline synthase (NOS) promoter and octopine synthase (OCS) promoters carried on tumor-inducing plasmids of Agrobacterium tumefaciens, caulimovirus promoters such as the cauliflower mosaic virus or Figwort mosaic virus promoters. For instance, see U.S. Pat. Nos. 5,858,742 and 5,322,938 which disclose versions of the constitutive promoter derived from cauliflower mosaic virus (CaMV35S), U.S. Pat. No. 5,378,619 which discloses a Figwort Mosaic Virus (FMV) 35S promoter, U.S. Pat. No. 6,437,217 which discloses a maize RS81 promoter, U.S. Pat. No. 5,641,876 which discloses a rice actin promoter, U.S. Pat. No. 6,426,446 which discloses a maize RS324 promoter, U.S. Pat. No. 6,429,362 which discloses a maize PR-1 promoter, U.S. Pat. No. 6,232,526 which discloses a maize A3 promoter, U.S. Pat. No. 6,177,611 which discloses constitutive maize promoters, U.S. Pat. No. 6,433,252 which discloses a maize L3 oleosin promoter, U.S. Pat. No. 6,429,357 which discloses a rice actin 2 promoter and intron, U.S. Pat. No. 5,837,848 which discloses a root specific promoter, U.S. Pat. No. 6,084,089 which discloses cold inducible promoters, U.S. Pat. No. 6,294,714 which discloses light inducible promoters, U.S. Pat. No. 6,140,078 which discloses salt inducible promoters, U.S. Pat. No. 6,252,138 which discloses pathogen inducible promoters, U.S. Pat. No. 6,175,060 which discloses phosphorus deficiency inducible promoters, U.S. Patent Application Publication 2002/0192813A1 which discloses 5′, 3′ and intron elements useful in the design of effective plant expression vectors, U.S. patent application Ser. No. 09/078,972 which discloses a coixin promoter, U.S. patent application Ser. No. 09/757,089 which discloses a maize chloroplast aldolase promoter, and U.S. patent application Ser. No. 10/739,565 which discloses water-deficit inducible promoters, all of which are incorporated herein by reference. These and numerous other promoters that function in plant cells are known to those skilled in the art and available for use in recombinant polynucleotides of the present invention to provide for expression of desired genes in transgenic plant cells.

Furthermore, the promoters can include multiple “enhancer sequences” to assist in elevating gene expression. Such enhancers are known in the art. By including an enhancer sequence with such constructs, the expression of the selected protein can be enhanced. These enhancers often are found 5′ to the start of transcription in a promoter that functions in eukaryotic cells, but can often be inserted in the forward or reverse orientation 5′ or 3′ to the coding sequence. In some instances, these 5′ enhancing elements are introns. Deemed to be particularly useful as enhancers are the 5′ introns of the rice actin 1 and rice actin 2 genes. Examples of other enhancers that can be used in accordance with the invention include elements from the CaMV 35S promoter, octopine synthase genes, the maize alcohol dehydrogenase gene, the maize shrunken 1 gene and promoters from non-plant cukaryotes.

In some aspects of the invention, the promoter element in the DNA construct can be capable of causing sufficient expression to result in the production of an effective amount of a polypeptide in water deficit conditions. Such promoters can be identified and isolated from the regulatory region of plant genes that are over expressed in water deficit conditions. Specific water-deficit-inducible promoters for use in this invention are derived from the 5′ regulatory region of genes identified as a heat shock protein 17.5 gene (HSP17.5), an HVA22 gene (HVA22), a Rab17 gene and a cinnamic acid 4-hydroxylase (CA4H) gcnc (CA44H) of Zea maize. Such water-deficit-inducible promoters are disclosed in U.S. application Ser. No. 10/739,565, incorporated herein by reference.

In some aspects of the invention, sufficient expression in plant seed tissues is desired to effect improvements in seed composition. Exemplary promoters for use for seed composition modification include promoters from seed genes such as napin (U.S. Pat. No. 5,420,034), maize L3 oleosin (U.S. Pat. No. 6,433,252), zein Z27 (Russell et al., (1997) Transgenic Res. 6(2):157-166), globulin 1 (Belanger et al., (1991) Genetics 129:863-872), glutelin 1 (Russell (1997) supra), and peroxiredoxin antioxidant (Perl) (Stacy et al., (1996) Plant Mol Biol. 31(6): 1205-1216).

In some aspects of the invention, expression in plant green tissues is desired. Promoters of interest for such uses include those from genes such as SSU (Fischhoff, et al., (1992) Plant Mol Biol. 20:81-93), aldolase and pyruvate orthophosphate dikinase (PPDK) (Taniguchi, et al., (2000) Plant Cell Physiol. 41(1):42-48).

Gene suppression includes any of the well-known methods for suppressing transcription of a gene or the accumulation of the mRNA corresponding to that gene thereby preventing translation of the transcript into protein. Posttranscriptional gene suppression is mediated by transcription of RNA that forms double-stranded RNA (dsRNA) having homology to a gene targeted for suppression. Suppression can also be achieved by insertion mutations created by transposable elements can also prevent gene function. For example, in many dicot plants, transformation with the T-DNA of Agrobacterium can be readily achieved and large numbers of transformants can be rapidly obtained. Also, some species have lines with active transposable elements that can efficiently be used for the generation of large numbers of insertion mutations, while some other species lack such options. Mutant plants produced by Agrobacterium or transposon mutagenesis and having altered expression of a polypeptide of interest can be identified using the polynucleotides of the present invention. For example, a large population of mutated plants can be screened with polynucleotides encoding the polypeptide of interest to detect mutated plants having an insertion in the gene encoding the polypeptide of interest.

Gene Stacking

The present invention also contemplates that the trait-improving recombinant DNA provided herein can be used in combination with other recombinant DNA to create plants with multiple desired traits or a further enhanced trait. The combinations generated can include multiple copies of any one or more of the recombinant DNA constructs. These stacked combinations can be created by any method, including but not limited to cross breeding of transgenic plants, or multiple genetic transformation.

Transformation Methods

Numerous methods for producing plant cell nuclei with recombinant DNA are known in the art and can be used in the present invention. Two commonly used methods for plant transformation are Agrobacterium-mediated transformation and microprojectile bombardment. Microprojectile bombardment methods are illustrated in U.S. Pat. No. 5,015,580 (soybean); U.S. Pat. No. 5,550,318 (corn); U.S. Pat. No. 5,538,880 (corn); U.S. Pat. No. 5,914,451 (soybean); U.S. Pat. No. 6,160,208 (corn); U.S. Pat. No. 6,399,861 (corn) and U.S. Pat. No. 6,153,812 (wheat) and Agrobacterium-mediated transformation is described in U.S. Pat. No. 5,159,135 (cotton); U.S. Pat. No. 5,824,877 (soybean); U.S. Pat. No. 5,463,174 (canola), U.S. Pat. No. 5,591,616 (corn); and U.S. Pat. No. 6,384,301 (soybean), all of which are incorporated herein by reference. For Agrobacterium tumefaciens based plant transformation system, additional elements present on transformation constructs will include T-DNA left and right border sequences to facilitate incorporation of the recombinant polynucleotide into the plant genome.

Numerous methods for transforming chromosomes in a plant cell nucleus with recombinant DNA are known in the art and are used in methods of preparing a transgenic plant cell nucleus cell, and plant. Two effective methods for such transformation are Agrobacterium-mediated transformation and microprojectile bombardment. Microprojectile bombardment methods are illustrated in U.S. Pat. No. 5,015,580 (soybean); U.S. Pat. No. 5,550,318 (corn); U.S. Pat. No. 5,538,880 (corn); U.S. Pat. No. 5,914,451 (soybean): U.S. Pat. No. 6,160,208 (corn); U.S. Pat. No. 6,399,861 (corn); U.S. Pat. No. 6,153,812 (wheat) and U.S. Pat. No. 6,365,807 (rice) and Agrobacterium-mediated transformation is described in U.S. Pat. No. 5,159,135 (cotton); U.S. Pat. No. 5,824,877 (soybean); U.S. Pat. No. 5,463,174 (canola, also known as rapeseed); U.S. Pat. No. 5,591,616 (corn); U.S. Pat. No. 6,384,301 (soybean), U.S. Pat. No. 7,026,528 (wheat) and U.S. Pat. No. 6,329,571 (rice), all of which are incorporated herein by reference for enabling the production of transgenic plants. Transformation of plant material is practiced in tissue culture on a nutrient media, i.e. a mixture of nutrients that will allow cells to grow in vitro. Recipient cell targets include, but arc not limited to, meristem cells, hypocotyls, calli, immature embryos and gametic cells such as microspores, pollen, sperm and egg cells. Callus may be initiated from tissue sources including, but not limited to, immature embryos, hypocotyls, seedling apical meristems, microspores and the like. Cells containing a transgenic nucleus are grown into transgenic plants.

In general it is useful to introduce heterologous DNA randomly, e.g., at a non-specific location, in the genome of a target plant line. In special cases it can be useful to target heterologous DNA insertion in order to achieve site-specific integration, e.g., to replace an existing gene in the genome, to use an existing promoter in the plant genome, or to insert a recombinant polynucleotide at a predetermined site known to be active for gene expression. Several site specific recombination systems exist which are known to function in plants including cre-lox as disclosed in U.S. Pat. No. 4,959,317 and FLP-FRT as disclosed in U.S. Pat. No. 5,527,695, both incorporated herein by reference.

Transformation methods of this invention can be practiced in tissue culture on media and in a controlled environment. “Media” refers to the numerous nutrient mixtures that are used to grow cells in vitro, that is, outside of the intact living organism. Recipient cell targets include, but are not limited to, meristem cells, calli, hypocotyles, immature embryos and gametic cells such as microspores, pollen, sperm and egg cells. It is contemplated that any cell from which a fertile plant can be regenerated is useful as a recipient cell. Callus can be initiated from tissue sources including, but not limited to, immature embryos, seedling apical meristems, microspores and the like. Cells capable of proliferating as callus are also recipient cells for genetic transformation. Practical transformation methods and materials for making transgenic plants of this invention, e.g., various media and recipient target cells, transformation of immature embryos and subsequent regeneration of fertile transgenic plants are disclosed in U.S. Pat. Nos. 6,194,636 and 6,232,526 and U.S. patent application Ser. No. 09/757,089, which are incorporated herein by reference.

The seeds of transgenic plants can be harvested from fertile transgenic plants and be used to grow progeny generations of transformed plants of this invention including hybrid plants line for selection of plants having an enhanced trait. In addition to direct transformation of a plant with a recombinant DNA, transgenic plants can be prepared by crossing a first plant having a recombinant DNA with a second plant lacking the DNA. For example, recombinant DNA can be introduced into a first plant line that is amenable to transformation to produce a transgenic plant which can be crossed with a second plant line to introgress the recombinant DNA into the second plant line. A transgenic plant with recombinant DNA providing an enhanced trait, e.g. enhanced yield, can be crossed with transgenic plant line having other recombinant DNA that confers another trait, for example herbicide resistance or pest resistance, to produce progeny plants having recombinant DNA that confers both traits. Typically, in such breeding for combining traits the transgenic plant donating the additional trait is a male line and the transgenic plant carrying the base traits is the female line. The progeny of this cross will segregate such that some of the plants will carry the DNA for both parental traits and some will carry DNA for one parental trait: such plants can be identified by markers associated with parental recombinant DNA, e.g. marker identification by analysis for recombinant DNA or, in the case where a selectable marker is linked to the recombinant, by application of the selecting agent such as a herbicide for use with a herbicide tolerance marker, or by selection for the enhanced trait. Progeny plants carrying DNA for both parental traits can be crossed back into the female parent line multiple times, for example usually 6 to 8 generations, to produce a progeny plant with substantially the same genotype as one original transgenic parental line but for the recombinant DNA of the other transgenic parental line.

In practice, DNA is introduced into only a small percentage of target cell nuclei. Marker genes are used to provide an efficient system for identification of those cells with nuclei that are stably transformed by receiving and integrating a recombinant DNA molecule into their genomes. Some marker genes provide selective markers that confer resistance to a selective agent, such as an antibiotic or herbicide. Potentially transformed cells with a nucleus of the invention are exposed to the selective agent. In the population of surviving cells will be those cells where, generally, the resistance-conferring gene has been integrated and expressed at sufficient levels to permit cell survival. Cells can be tested further to confirm stable integration of the exogenous DNA in the nucleus. Useful selective marker genes include those conferring resistance to antibiotics such as kanamycin (nptII), hygromycin B (aph IV), spectinomycin (aadA) and gentamycin (aac3 and aacC4) or resistance to herbicides such as glufosinate (bar or pat), dicamba (DMO) and glyphosate (EPSPS). Examples of such selectable markers are illustrated in U.S. Pat. Nos. 5,550,318; 5,633,435; 5,780,708 and 6,118,047, all of which are incorporated herein by reference. Screenable markers which provide an ability to visually identify transformants can also be employed, e.g., a gene expressing a colored or fluorescent protein such as a luciferase or green fluorescent protein (GFP) or a gene expressing a beta-glucuronidase or uidA gene (GUS) for which various chromogenic substrates are known. It is also contemplated that combinations of screenable and selectable markers will be useful for identification of transformed cells. See PCT publication WO 99/61129 (herein incorporated by reference) which discloses use of a gene fusion between a selectable marker gene and a screenable marker gene, e.g., an NPTII gene and a GFP gene.

Plant cells that survive exposure to the selective agent, or cells that have been scored positive in a screening assay, can be cultured in regeneration media and allowed to mature into plants. Developing plantlets can be transferred to soil less plant growth mix, and hardened off, e.g., in an environmentally controlled chamber at about 85% relative humidity, 600 ppm CO₂, and 25-250 microeinsteins m⁻² s⁻¹ of light, prior to transfer to a greenhouse or growth chamber for maturation. Plants are matured either in a growth chamber or greenhouse. Plants are regenerated from about 6 weeks to 10 months after a transformant is identified, depending on the initial tissue. During regeneration, cells are grown to plants on solid media at about 19 to 28° C. After regenerating plants have reached the stage of shoot and root development, they can be transferred to a greenhouse for further growth and testing. Plants can be pollinated using conventional plant breeding methods known to those of skill in the art and seed produced.

Progeny can be recovered from transformed plants and tested for expression of the exogenous recombinant polynucleotide. Useful assays include, for example, “molecular biological” assays, such as Southern and Northern blotting and PCR; “biochemical” assays, such as detecting the presence of RNA, e.g., double stranded RNA, or a protein product, e.g., by immunological means (ELISAs and Western blots) or by enzymatic function; plant part assays, such as leaf or root assays; and also, by analyzing the phenotype of the whole regenerated plant.

Discovery of Trait-Improving Recombinant DNA

To identify nuclei with recombinant DNA that confer enhanced traits to plants, Arabidopsis thaliana was transformed with a candidate recombinant DNA construct and screened for an enhanced trait.

Arabidopsis thaliana is used a model for genetics and metabolism in plants. A two-step screening process was employed which included two passes of trait characterization to ensure that the trait modification was dependent on expression of the recombinant DNA, but not duc to the chromosomal location of the integration of the transgene. Twelve independent transgenic lines for each recombinant DNA construct were established and assayed for the transgene expression levels. Five transgenic lines with high transgene expression levels were used in the first pass screen to evaluate the transgene's function in T2 transgenic plants. Subsequently, three transgenic events, which had been shown to have one or more enhanced traits, were further evaluated in the second pass screen to confirm the transgene's ability to impart an enhanced trait. The following Table 3 summarizes the enhanced traits that have been confirmed as provided by a recombinant DNA construct.

In particular, Table 3 reports:

“PEP SEQ ID” which is the amino acid sequence of the protein corresponding to the DNA in the recombinant DNA construct corresponding to a protein sequence of a SEQ ID NO. in the Sequence Listing.

“construct_id” is an arbitrary name for the recombinant DNA describe more particularly in Table 1.

“annotation” refers to a description of the top hit protein obtained from an amino acid sequence query of each PEP SEQ ID NO to GenBank database of the National Center for Biotechnology Information (ncbi). More particularly, “gi” is the GenBank ID number for the top BLAST hit.

“description” refers to the description of the top BLAST hit.

“e-value” provides the expectation value for the BLAST hit.

“% id” refers to the percentage of identically matched amino acid residues along the length of the portion of the sequences which is aligned by BLAST between the sequence of interest provided herein and the hit sequence in GenBank.

“traits” identify by two letter codes the confirmed enhancement in a transgenic plant provided by the recombinant DNA. The codes for enhanced traits are:

“CK” which indicates cold tolerance enhancement identified under a cold shock tolerance screen;

“CS” which indicates cold tolerance enhancement identified by a cold germination tolerance screen;

“DS” which indicates drought tolerance enhancement identified by a soil drought stress tolerance screen;

“PEG” which indicates osmotic stress tolerance enhancement identified by a PEG induced osmotic stress tolerance screen;

“HS” which indicates heat stress tolerance enhancement identified by a heat stress tolerance screen;

“SS” which indicates high salinity stress tolerance enhancement identified by a salt stress tolerance screen;

“LN” which indicates nitrogen use efficiency enhancement identified by a limited nitrogen tolerance screen;

“LL” which indicates attenuated shade avoidance response identified by a shade tolerance screen under a low light condition;

“PP” which indicates enhanced growth and development at early stages identified by an early plant growth and development screen;

“SP” which indicates enhanced growth and development at late stages identified by a late plant growth and development screen provided herein.

TABLE 3 NUC PEP Seq Seq ID ID Annotation No. Gene ID No. E-value % id Description Traits 1 CGPG113 140 0 90 gb|AAA86281.1|CKC HS 2 CGPG1754 141 1.00E−156 78 ref|NP_564784.1|DNA-binding storekeeper protein-related PP [Arabidopsis thaliana] 3 CGPG1809 142 1.00E−105 76 ref|NP_200116.1|RWP-RK domain-containing protein [Arabidopsis SP thaliana] 4 CGPG2053 143 1.00E−124 82 gb|AAD22130.2|expressed protein [Arabidopsis thaliana] SS 5 CGPG2164 144 0 93 gb|AAG53999.1|AF336918_1ARF2 [Arabidopsis thaliana] SS 6 CGPG2551 145 3.00E−92 81 ref|NP_172518.1|ZFP5 (ZINC FINGER PROTEIN 5); nucleic acid LL binding/transcription factor/zinc ion binding [Arabidopsis thaliana] 7 CGPG2578 146 1.00E−139 95 ref|NP_187963.1|ATMYB5 (myb domain protein 5); DNA binding/ SS transcription factor [Arabidopsis thaliana] 8 CGPG2583 147 1.00E−112 100 pir||H84613probable MADS-box protein [imported] - Arabidopsis PP PEG thaliana 9 CGPG2586 148 1.00E−107 79 ref|NP_177524.2|BEE3 (BR ENHANCED EXPRESSION 3); DNA PEG binding/transcription factor [Arabidopsis thaliana] 10 CGPG2593 149 1.00E−147 84 ref|NP_188962.2|basic helix-loop-helix (bHLH) family protein PP [Arabidopsis thaliana] 11 CGPG2594 150 0 83 sp|Q9LEZ3|BIM1_ARATHTranscription factor BIM1 (BES1-interacting SS Myc-like protein 1) (Transcription factor EN 126) (Basic helix-loop- helix protein 46) 12 CGPG26 151 1.00E−134 94 ref|NP_177074.1|AP1 (APETALA1); DNA binding/transcription factor LN [Arabidopsis thaliana] 13 CGPG2604 152 1.00E−151 100 ref|NP_187737.1|myb family transcription factor [Arabidopsis thaliana] LN 14 CGPG2615 153 1.00E−178 92 ref|NP_177338.1|VND7 (VASCULAR RELATED NAC-DOMAIN HS PROTEIN 7); transcription factor [Arabidopsis thaliana] 15 CGPG2639 154 5.00E−91 60 ref|NP_566232.1|DNA-binding protein-related [Arabidopsis thaliana] DS 16 CGPG2644 155 1.00E−174 88 ref|NP_189199.1|basic helix-loop-helix (bHLH) family protein HS [Arabidopsis thaliana] 17 CGPG2657 156 1.00E−102 77 ref|NP_188666.1|ERF7 (ETHYLINE RESPONSE FACTOR7); DNA PP SP binding/protein binding/transcription factor/transcriptional repressor [Arabidopsis thaliana] 18 CGPG2664 157 2.00E−69 100 ref|NP_188827.1|zinc finger (B-box type) family protein [Arabidopsis PEG PP thaliana] 19 CGPG2678 158 1.00E−110 94 ref|NP_564263.1|zinc finger (C3HC4-type RING finger) family protein CK [Arabidopsis thaliana] 20 CGPG2699 159 0 91 ref|NP_200853.1|ARF4 (AUXIN RESPONSE FACTOR 4); CK transcription factor [Arabidopsis thaliana] 21 CGPG2704 160 0 100 ref|NP_001030821.1|TRFL1 (TRF-LIKE 1); DNA binding [Arabidopsis DS LL thaliana] 22 CGPG2711 161 0 94 ref|NP_191351.1|squamosa promoter-binding protein, putative DS [Arabidopsis thaliana] 23 CGPG2735 162 1.00E−102 100 ref|NP_191211.1|no apical meristem (NAM) family protein HS [Arabidopsis thaliana] 24 CGPG2752 163 1.00E−176 100 ref|NP_172279.1|zinc finger (GATA type) family protein [Arabidopsis SS thaliana] 25 CGPG2757 164 0 96 ref|NP_171609.1|ANAC001 (Arabidopsis NAC domain containing PP protein 1); transcription factor [Arabidopsis thaliana] 26 CGPG2767 165 0 65 ref|NP_175412.1|zinc finger (C2H2 type) family protein [Arabidopsis PP SS thaliana] 27 CGPG2778 166 0 100 ref|NP_197640.1|zinc finger (ZPR1-type) family protein [Arabidopsis SS thaliana] 28 CGPG2797 167 0 92 dbj|BAF62149.1|C2—H2 zinc finger protein [Arabidopsis thaliana] PP 29 CGPG2805 168 1.00E−167 100 ref|NP_564230.1|MYB116 (myb domain protein 116); DNA binding/ DS HS transcription factor [Arabidopsis thaliana] 30 CGPG2811 169 1.00E−158 79 gb|AAG50818.1|AC079281_20hypothetical protein [Arabidopsis DS HS thaliana] 31 CGPG2907 170 0 86 gb|AAF99784.1|AC012463_1T2E6.3 [Arabidopsis thaliana] HS 32 CGPG2935 171 1.00E−57 100 ref|NP_200132.2|TRY (TRIPTYCHON); DNA binding/transcription DS factor [Arabidopsis thaliana] 33 CGPG2943 172 0 95 gb|AAF25987.1|AC013354_6F15H18.16 [Arabidopsis thaliana] CK HS 34 CGPG2948 173 1.00E−167 94 ref|NP_198065.2|MADS-box family protein [Arabidopsis thaliana] CS HS PP 35 CGPG2961 174 1.00E−146 80 ref|NP_189218.1|AP2 domain-containing transcription factor, putative PP SS [Arabidopsis thaliana] 36 CGPG2975 175 2.00E−97 91 ref|NP_850951.2|KNAT6 (Knotted-like Arabidopsis thaliana 6); DNA CK binding/transcription factor s 37 CGPG2985 176 1.00E−127 79 ref|NP_201559.1|ATTRB2/TRB2 (TELOMERE REPEAT BINDING HS FACTOR 2); DNA binding/transcription factor [Arabidopsis thaliana] 38 CGPG3107 177 0 97 ref|NP_566442.1|myb family transcription factor [Arabidopsis thaliana] HS 39 CGPG3169 178 1.00E−118 100 ref|NP_196979.1|WER (WEREWOLF 1); DNA binding/transcription HS factor [Arabidopsis thaliana] 40 CGPG3171 179 1.00E−128 95 ref|NP_197898.1|ZFP3 (ZINC FINGER PROTEIN 3); nucleic acid HS binding/transcription factor/zinc ion binding [Arabidopsis thaliana] 41 CGPG3175 180 1.00E−116 81 ref|NP_182191.1|ATHB-7 (ARABIDOPSIS THALIANA HOMEOBOX HS 7); transcription factor [Arabidopsis thaliana] 42 CGPG3287 181 1.00E−180 86 ref|NP_566101.1|CAO (CHAOS); chromatin binding [Arabidopsis PP thaliana] 43 CGPG3289 182 1.00E−65 86 ref|NP_566290.1|zinc finger (GATA type) family protein [Arabidopsis CS HS thaliana 44 CGPG3296 183 0 77 ref|NP_564359.1|WRKY14 (WRKY DNA-binding protein 14); SS transcription factor [Arabidopsis thaliana] 45 CGPG3298 184 1.00E−172 92 ref|NP_564486.1|VIP1 (VIRE2-INTERACTING PROTEIN 1); DS LL transcription factor [Arabidopsis thaliana] 46 CGPG3309 185 1.00E−118 94 ref|NP_178188.1|ZFP1 (ARABIDOPSIS THALIANA ZINC-FINGER HS PROTEIN 1); nucleic acid binding/transcription factor/zinc ion binding [Arabidopsis thaliana] 47 CGPG3312 186 1.00E−174 86 ref|NP_181594.1|bZIP transcription factor family protein [Arabidopsis PP thaliana] 48 CGPG3327 187 2.00E−87 88 ref|NP_172872.1|zinc finger (C3HC4-type RING finger) family protein HS [Arabidopsis thaliana] 49 CGPG3341 188 0 85 ref|NP_195410.1|AP2 (APETALA 2); transcription factor [Arabidopsis LN thaliana] 50 CGPG3347 189 5.00E−82 74 ref|NP_566567.1|transcription factor [Arabidopsis thaliana] PP 51 CGPG3369 190 0 91 ref|NP_175475.2|SCL5; transcription factor [Arabidopsis thaliana] CK HS 52 CGPG3449 191 1.00E−122 62 ref|NP_193820.1|ethylene-responsive nuclear protein/ethylene- SS regulated nuclear protein (ERT2) [Arabidopsis thaliana] 53 CGPG3451 192 1.00E−113 94 ref|NP_194271.1|basix helix-loop-helix (bHLH) family protein HS [Arabidopsis thaliana] 54 CGPG3463 193 0 87 ref|NP_200855.1|zinc finger (C2H2 type) family protein [Arabidopsis HS thaliana] 55 CGPG3468 194 1.00E−176 95 ref|NP_001031160.1|zinc ion binding [Arabidopsis thaliana] LN 56 CGPG3476 195 4.00E−92 72 ref|NP_177887.1|AP2 domain-containing transcription factor, putative LN [Arabidopsis thaliana] 57 CGPG3505 196 0 100 gb|AAF05867.1|AC011698_18transfactor-like [Arabidopsis thaliana] CS HS 58 CGPG359 197 4.00E−95 100 ref|NP_176569.1|zinc finger (C3HC4-type RING finger) family protein LL [Arabidopsis thaliana] 59 CGPG367 198 1.00E−132 86 ref|NP_177583.1|MYB95 (myb domain protein 95); DNA binding/ PEG transcription factor [Arabidopsis thaliana] 60 CGPG3750 199 0 83 ref|NP_172690.1|VND4 (VASCULAR RELATED NAC-DOMAIN SS PROTEIN 4); transcription factor [Arabidopsis thaliana] 61 CGPG3761 200 0 98 ref|NP_190564.1|scarecrow transcription factor family protein HS SP [Arabidopsis thaliana] 62 CGPG3793 201 1.00E−164 93 ref|NP_199078.1|zinc finger (C2H2 type) family protein [Arabidopsis HS thaliana] 63 CGPG3795 202 0 92 ref|NP_173950.1|basic helix-loop-helix (bHLH) family protein HS PEG [Arabidopsis thaliana] 64 CGPG3804 203 1.00E−147 90 ref|NP_174279.1|WRKY71 (WRKY DNA-binding protein 71); HS transcription factor [Arabidopsis thaliana] 65 CGPG3810 204 1.00E−166 83 ref|NP_174494.2|bZIP transcription factor family protein [Arabidopsis CS HS thaliana] 66 CGPG3813 205 0 100 ref|NP_174554.1|ANAC012/NST3/SND1 (ARABIDOPSIS NAC HS DOMAIN CONTAINING PROTEIN 12, NAC SECONDARY WALL THICKENING PROMOTING 3); transcription factor/transcriptional activator [Arabidopsis thaliana] 67 CGPG382 206 0 90 gb|AAG52391.1|AC011915_5putative B-box zinc finger protein; LN 52092-50677 [Arabidopsis thaliana] 68 CGPG3825 207 1.00E−144 100 ref|NP_176829.1|WRKY64 (WRKY DNA-binding protein 64); CS PEG transcription factor [Arabidopsis thaliana] 69 CGPG3828 208 1.00E−151 74 ref|NP_177346.1|TCP family transcription factor, putative [Arabidopsis CS HS thaliana] 70 CGPG3837 209 1.00E−177 92 ref|NP_179176.1|zinc finger (C2H2 type) family protein [Arabidopsis HS thaliana] 71 CGPG3841 210 0 85 ref|NP_180679.2|basic helix-loop-helix (bHLH) family protein HS [Arabidopsis thaliana] 72 CGPG3843 211 0 89 ref|NP_181555.1|myb family transcription factor [Arabidopsis thaliana] HS PEG 73 CGPG3857 212 1.00E−133 89 ref|NP_001077812.1|ethylene-responsive element-binding protein, CS HS putative [Arabidopsis thaliana]] 74 CGPG3858 213 1.00E−112 75 ref|NP_177090.1|WRKY57 (WRKY DNA-binding protein 57); CS transcription factor [Arabidopsis thaliana] 75 CGPG3865 214 2.00E−96 83 ref|NP_195806.1|zinc finger (C2H2 type) family protein [Arabidopsis HS thaliana 76 CGPG3868 215 9.00E−78 86 ref|NP_199895.3|ANAC097 (Arabidopsis NAC domain containing HS protein 97); transcription factor [Arabidopsis thaliana] 77 CGPG3869 216 1.00E−139 95 ref|NP_188400.1|ANAC057 (Arabidopsis NAC domain containing CK protein 57); transcription factor [Arabidopsis thaliana] 78 CGPG3875 217 0 82 gb|AAF26166.1|AC008261_23putative DNA-binding protein PP [Arabidopsis thaliana] 79 CGPG3879 218 0 80 ref|NP_027544.1|myb family transcription factor [Arabidopsis thaliana] LN PP 80 CGPG3947 219 2.00E−92 74 gb|AAX13296.1|MADS box protein AP1a [Lotus corniculatus var. PP japonicus] 81 CGPG3987 220 2.00E−75 99 gb|ABH02834.1|MYB transcription factor MYB178 [Glycine max] HS 82 CGPG4004 221 1.00E−104 56 emb|CAO43809.1|unnamed protein product [Vitis vinifera] HS 83 CGPG4013 222 1.00E−126 74 gb|AAQ57226.1|DREB2 [Glycine max] HS 84 CGPG4015 223 1.00E−136 87 dbj|BAA81733.2|GmMYB29A2 [Glycine max] HS LL 85 CGPG4061 224 1.00E−113 59 emb|CAN68564.1|hypothetical protein [Vitis vinifera] PP 86 CGPG4066 225 1.00E−134 75 gb|AAK84889.1|AF402608_1TGA-type basic leucine zipper protein LL TGA2.1 [Phaseolus vulgaris] 87 CGPG4082 226 3.00E−88 56 emb|CAO17657.1|unnamed protein product [Vitis vinifera] HS 88 CGPG4106 227 1.00E−103 67 ref|NP_171677.1|ATAF1 (Arabidopsis NAC domain containing protein HS 2); transcription factor [Arabidopsis thaliana] 89 CGPG4112 228 2.00E−87 64 emb|CAO67297.1|unnamed protein product [Vitis vinifera] CS 90 CGPG4133 229 1.00E−132 85 emb|CAA87077.1|heat shock transcription factor 34 [Glycine max] CK PP 91 CGPG4166 230 1.00E−122 66 emb|CAO43957.1|unnamed protein product [Vitis vinifera] DS 92 CGPG4195 231 1.00E−143 85 gb|ABK92551.1|unknown [Populus trichocarpa] HS 93 CGPG4525 232 0 91 ref|NP_180366.1|BLH8 (BEL1-LIKE HOMEODOMAIN 8); DNA HS binding/transcription factor [Arabidopsis thaliana] 94 CGPG4527 233 1.00E−138 79 emb|CAL64011.1|BRANCHED2 [Arabidopsis thaliana] LL 95 CGPG4537 234 1.00E−175 78 ref|NP_176237.1|apical meristem formation protein-related LL [Arabidopsis thaliana 96 CGPG4591 235 1.00E−98 80 ref|NP_188752.1|zinc finger (B-box type) family protein [Arabidopsis SS PEG thaliana] 97 CGPG4612 236 1.00E−157 93 ref|NP_174529.2|ANAC011 (Arabidopsis NAC domain containing LL protein 11); transcription factor [Arabidopsis thaliana] 98 CGPG4632 237 5.00E−58 89 ref|NP_194270.1|basix helix-loop-helix (bHLH) family protein CS LL [Arabidopsis thaliana] 99 CGPG490 238 1.00E−127 68 gb|AAZ66389.1|RAV-like DNA-binding protein [Glycine max] LL 100 CGPG5130 239 1.00E−173 82 ref|NP_176536.2|DNA-binding family protein [Arabidopsis thaliana] CK DS 101 CGPG5278 240 2.00E−98 55 emb|CAO15010.1|unnamed protein product [Vitis vinifera] DS 102 CGPG5280 241 1.00E−110 83 ref|NP_001031695.1|DNA binding [Arabidopsis thaliana] LL 103 CGPG5292 242 1.00E−104 69 gb|ABH02859.1|MYB transcription factor MYB138 [Glycine max] LL 104 CGPG5306 243 3.00E−68 55 emb|CAA67968.1|MADS4 protein [Betula pendula] HS PP LN 105 CGPG5316 244 0 60 emb|CAO15649.1|unnamed protein product [Vitis vinifera] LN 106 CGPG5324 245 3.00E−47 60 sp|Q00423|HMGYA_SOYBNHMG-Y-related protein A (Protein LN SP SB16A) 107 CGPG5330 246 2.00E−44 50 gb|ABD64947.1|ethylene responsive element binding factor, putative HS [Brassica oleracea] 108 CGPG5334 247 1.00E−174 88 gb|ABH02830.1|MYB transcription factor MYB62 [Glycine max] HS 109 CGPG5422 248 0 89 ref|NP_172900.2|protein binding [Arabidopsis thaliana] DS 110 CGPG5599 249 0 95 ref|NP_179306.2|RWP-RK domain-containing protein [Arabidopsis PP thaliana] 111 CGPG690 250 1.00E−113 80 ref|NP_189865.1|PHD finger family protein [Arabidopsis thaliana] CK 112 CGPG7354 251 2.00E−93 68 gb|ABY84652.1|transcription factor [Glycine max] CS 113 CGPG7367 252 1.00E−131 67 emb|CAC84706.1|aux/IAA protein [Populus tremula x Populus PEG tremuloides] 114 CGPG7369 253 1.00E−154 89 gb|ABI16022.1|Dof21 [Glycine max] PEG 115 CGPG7373 254 1.00E−68 47 emb|CAN72162.1|hypothetical protein [Vitis vinifera] LN 116 CGPG7374 255 1.00E−107 53 gb|ABK20308.1|Myb transcription factor [Malus x domestica] LL 117 CGPG7376 256 1.00E−130 90 gb|ABS18444.1|WRKY48 [Glycine max] LN 118 CGPG7378 257 2.00E−86 57 emb|CAO23794.1|unnamed protein product [Vitis vinifera] DS 119 CGPG7641 258 1.00E−111 65 emb|CAN62363.1|hypothetical protein [Vitis vinifera] LL 120 CGPG7655 259 4.00E−50 48 emb|CAO61053.1|unnamed protein product [Vitis vinifera] LL 121 CGPG7678 260 1.00E−125 86 gb|ABH02860.1|MYB transcription factor MYB139 [Glycine max] LL 122 CGPG7697 261 0 96 gb|AAX85980.1|NAC3 protein [Glycine max] LN 123 CGPG7709 262 2.00E−65 68 emb|CAO46779.1|unnamed protein product [Vitis vinifera] SP 124 CGPG7714 263 1.00E−94 92 sp|P13088|AUX22_SOYBNAuxin-induced protein AUX22 CS LL 125 CGPG7743 264 6.00E−37 45 ref|NP_201280.1|ABR1 (ABA REPRESSOR1); DNA binding/ SS LN transcription factor [Arabidopsis thaliana] 126 CGPG7748 265 0 70 emb|CAO68379.1|unnamed protein product [Vitis vinifera] CK 127 CGPG7757 266 0 81 sp|O04235|SSRP1_VICFAFACT complex subunit SSRP1 (Facilitates CS PEG chromatin transcription complex subunit SSRP1) (Recombination signal sequence recognition protein 1) 128 CGPG7759 267 9.00E−64 73 emb|CAO44022.1|unnamed protein product [Vitis vinifera] LL 129 CGPG7822 268 9.00E−99 70 emb|CAN77695.1|hypothetical protein [Vitis vinifera] DS 130 CGPG7840 269 6.00E−75 40 ref|NP_188826.1|zinc finger (B-box type) family protein [Arabidopsis DS thaliana] 131 CGPG7876 270 1.00E−45 46 gb|AAD09248.1|EREBP-3 homolog [Stylosanthes hamata] CK 132 CGPG858 271 0 91 ref|NP_566718.2|TSO1 (CHINESE FOR ‘UGLY’); transcription factor HS [Arabidopsis thaliana] dbj|BAB01253.1|DNA binding protein-like [Arabidopsis thaliana] 133 CGPG2562 272 0 88 ref|NP_176964.1|AT-HSFA8 (Arabidopsis thaliana heat shock PEG transcription factor A8); DNA binding/transcription factor 134 CGPG31 273 0 88 ref|NP_188713.1|EIN3 (ETHYLENE-INSENSITIVE3); transcription SS factor [Arabidopsis thaliana] 135 CGPG4213 274 1.00E−113 85 ref|NP_181549.1|basic helix-loop-helix (bHLH) family protein LN [Arabidopsis thaliana] 136 CGPG477 275 5.00E−56 71 ref|NP_196837.1|RAP2.6L (related to AP2 6L); DNA binding/ LN transcription factor [Arabidopsis thaliana] 137 CGPG6312 276 0 76 ref|NP_190697.1|proline-rich family protein [Arabidopsis thaliana] LL 138 CGPG7188 277 1.00E−121 79 ref|NP_564491.1|transcription regulator [Arabidopsis thaliana] HS 139 CGPG8726 278 1.00E−124 94 gb|AAY78741.1|DNA-binding protein-related [Arabidopsis thaliana] HS

Trait Enhancement Screens

DS-Enhancement of Drought Tolerance Identified by a Soil Drought Stress Tolerance Screen:

Drought or water deficit conditions impose mainly osmotic stress on plants. Plants are particularly vulnerable to drought during the flowering stage. The drought condition in the screening process disclosed in Example 1B started from the flowering time and was sustained to the end of harvesting. The present invention provides recombinant DNA that can improve the plant survival rate under such sustained drought condition. Exemplary recombinant DNA for conferring such drought tolerance are identified as such in Table 3. Such recombinant DNA can be used in generating transgenic plants that are tolerant to the drought condition imposed during flowering time and in other stages of the plant life cycle. As demonstrated from the model plant screen, in some embodiments of transgenic plants with trait-improving recombinant DNA grown under such sustained drought condition can also have increased total seed weight per plant in addition to the increased survival rate within a transgenic population, providing a higher yield potential as compared to control plants.

PEG-Enhancement of Drought Tolerance Identified by PEG Induced Osmotic Stress Tolerance Screen:

Various drought levels can be artificially induced by using various concentrations of polyethylene glycol (PEG) to produce different osmotic potentials (Pilon-Smits e.g., (1995) Plant Physiol. 107:125-130). Several physiological characteristics have been reported as being reliable indications for selection of plants possessing drought tolerance. These characteristics include the rate of seed germination and seedling growth. The traits can be assayed relatively easily by measuring the growth rate of seedling in PEG solution. Thus, a PEG-induced osmotic stress tolerance screen is a useful surrogate for drought tolerance screen. As demonstrated from the model plant screen, embodiments of transgenic plants with trait-improving recombinant DNA identified in the PEG-induced osmotic stress tolerance screen can survive better drought conditions providing a higher yield potential as compared to control plants.

SS-Enhancement of Drought Tolerance Identified by High Salinity Stress Tolerance Screen:

Three different factors are responsible for salt damages: (1) osmotic effects, (2) disturbances in the mineralization process, and (3) toxic effects caused by the salt ions, e.g., inactivation of enzymes. While the first factor of salt stress results in the wilting of the plants that is similar to drought effect, the ionic aspect of salt stress is clearly distinct from drought. The present invention provides genes that help plants maintain biomass, root growth, and/or plant development in high salinity conditions, which are identified as such in Table 3. Since osmotic effect is one of the major components of salt stress, which is common to the drought stress, trait-improving recombinant DNA identified in a high salinity stress tolerance screen can also provide transgenic crops with enhanced drought tolerance. As demonstrated from the model plant screen, embodiments of transgenic plants with trait-improving recombinant DNA identified in a high salinity stress tolerance screen can survive better drought conditions and/or high salinity conditions providing a higher yield potential as compared to control plants.

HS-Enhancement of Drought Tolerance Identified by Heat Stress Tolerance Screen:

Heat and drought stress often occur simultaneously, limiting plant growth. Heat stress can cause the reduction in photosynthesis rate, inhibition of leaf growth and osmotic potential in plants. Thus, genes identified by the present invention as heat stress tolerance conferring genes can also impart enhanced drought tolerance to plants. As demonstrated from the model plant screen, embodiments of transgenic plants with trait-improving recombinant DNA identified in a heat stress tolerance screen can survive better heat stress conditions and/or drought conditions providing a higher yield potential as compared to control plants.

CK and CS-Enhancement of Tolerance to Cold Stress:

Low temperature can immediately result in mechanical constraints, changes in activities of macromolecules, and reduced osmotic potential. In the present invention, two screening conditions, e.g., cold shock tolerance screen (CK) and cold germination tolerance screen (CS), were set up to look for transgenic plants that display visual growth advantage at lower temperature. In cold germination tolerance screen, the transgenic Arabidopsis plants were exposed to a constant temperature of 8° C. from planting until day 28 post plating. The trait-improving recombinant DNA identified by such screen are particular useful for the production of transgenic plant that can germinate more robustly in a cold temperature as compared to the wild type plants. In cold shock tolerance screen, the transgenic plants were first grown under the normal growth temperature of 22° C. until day 8 post plating, and subsequently were placed under 8° C. until day 28 post plating. As demonstrated from the model plant screen, embodiments of transgenic plants with trait-improving recombinant DNA identified in a cold shock stress tolerance screen and/or a cold germination stress tolerance screen can survive better cold conditions providing a higher yield potential as compared to control plants.

Enhancement of Tolerance to Multiple Stresses:

Different kinds of stresses often lead to identical or similar reaction in the plants. Genes that are activated or inactivated as a reaction to stress can either act directly in a way the genetic product reduces a specific stress, or they can act indirectly by activating other specific stress genes. By manipulating the activity of such regulatory genes, e.g., multiple stress tolerance genes, the plant can be enabled to react to different kinds of stresses. For examples, PEP SEQ ID NO:172 can be used to enhance both cold chock tolerance and heat stress tolerance in plants. Of particular interest, plants transformed with PEP SEQ ID NO: 235 can resist salt and osmotic stress. Plants transformed with PEP SEQ ID NO: 243 can also improve growth in early stage and under heat stress. In addition to these multiple stress tolerance genes, the stress tolerance conferring genes provided by the present invention may be used in combinations to generate transgenic plants that can resist multiple stress conditions.

PP-Enhancement of Early Plant Growth and Development:

It has been known in the art that to minimize the impact of disease on crop profitability, it is important to start the season with healthy and vigorous plants. This means avoiding seed and seedling diseases, leading to increased nutrient uptake and increased yield potential. Traditionally early planting and applying fertilizer are the methods used for promoting early seedling vigor. In early development stage, plant embryos establish only the basic root-shoot axis, a cotyledon storage organ(s), and stem cell populations, called the root and shoot apical meristems that continuously generate new organs throughout post-embryonic development. “Early growth and development” used herein encompasses the stages of seed imbibition through the early vegetative phase. The present invention provides genes that are useful to produce transgenic plants that have advantages in one or more processes including, but not limited to, germination, seedling vigor, root growth and root morphology under non-stressed conditions. The transgenic plants starting from a more robust seedling are less susceptible to the fungal and bacterial pathogens that attach germinating seeds and seedling. Furthermore, seedlings with advantage in root growth are more resistant to drought stress due to extensive and deeper root architecture. Therefore, it can be recognized by those skilled in the art that genes conferring the growth advantage in early stages to plants can also be used to generate transgenic plants that are more resistant to various stress conditions due to enhanced early plant development. The present invention provides such exemplary recombinant DNA that confer both the stress tolerance and growth advantages to plants, identified as such in Table 3, e.g., PEP SEQ ID NO: 173 which can improve the plant early growth and development, and impart salt tolerance to plants. As demonstrated from the model plant screen, embodiments of transgenic plants with trait-improving recombinant DNA identified in the early plant development screen can grow better under non-stress conditions and/or stress conditions providing a higher yield potential as compared to control plants.

SP-Enhancement of Late Plant Growth and Development:

“Late growth and development” used herein encompasses the stages of leaf development, flower production, and seed maturity. In certain embodiments, transgenic plants produced using genes that confer growth advantages to plants provided by the present invention, identified as such in Table 3, exhibit at least one phenotypic characteristics including, but not limited to, increased rosette radius, increased rosette dry weight, seed dry weight, silique dry weight, and silique length. On one hand, the rosette radius and rosette dry weight are used as the indexes of photosynthesis capacity, and thereby plant source strength and yield potential of a plant. On the other hand, the seed dry weight, silique dry weight and silique length are used as the indexes for plant sink strength, which are considered as the direct determinants of yield. As demonstrated from the model plant screen, embodiments of transgenic plants with trait-improving recombinant DNA identified in the late development screen can grow better and/or have enhanced development during leaf development and seed maturation providing a higher yield potential as compared to control plants.

LL-Enhancement of Tolerance to Shade Stress Identified in a Low Light Screen:

The effects of light on plant development are especially prominent at the seedling stage. Under normal light conditions with unobstructed direct light, a plant seeding develops according to a characteristic photomorphogenic pattern, in which plants have open and expanded cotyledons and short hypocotyls. Then the plant's energy is devoted to cotyledon and leaf development while longitudinal extension growth is minimized. Under low light condition where light quality and intensity are reduced by shading, obstruction or high population density, a seedling displays a shade-avoidance pattern, in which the seedling displays a reduced cotyledon expansion, and hypocotyls extension is greatly increased. As the result, a plant under low light condition increases significantly its stem length at the expanse of leaf, seed or fruit and storage organ development, thereby adversely affecting of yield. The present invention provides recombinant DNA that enable plants to have an attenuated shade avoidance response so that the source of plant can be contributed to reproductive growth efficiently, resulting higher yield as compared to the wild type plants. As demonstrated from the model plant screen, embodiments of transgenic plants with trait-improving recombinant DNA identified in a shade stress tolerance screen can have attenuated shade response under shade conditions providing a higher yield potential as compared to control plants. The transgenic plants generated by the present invention can be suitable for a higher density planting, thereby resulting increased yield per unit area.

LN-Enhancement of Tolerance to Low Nitrogen Availability Stress

Nitrogen is a key factor in plant growth and crop yield. The metabolism, growth and development of plants are profoundly affected by their nitrogen supply. Restricted nitrogen supply alters shoot to root ratio, root development, activity of enzymes of primary metabolism and the rate of senescence (death) of older leaves. All field crops have a fundamental dependence on inorganic nitrogenous fertilizer. Since fertilizer is rapidly depleted from most soil types, it must be supplied to growing crops two or three times during the growing season. Enhanced nitrogen use efficiency by plants should enable crops cultivated under low nitrogen availability stress condition resulted from low fertilizer input or poor soil quality.

This invention demonstrates that the transgenic plants generated using the recombinant nucleotides, which confer enhanced nitrogen use efficiency, identified as such in Table 3, exhibit one or more desirable traits including, but not limited to, increased seedling weight, greener leaves, increased number of rosctte leaves, increased or decreased root length. One skilled in the art can recognize that the transgenic plants provided by the present invention with enhanced nitrogen use efficiency can also have altered amino acid or protein compositions, increased yield and/or better seed quality. The transgenic plants of the present invention can be productively cultivated under low nitrogen growth conditions, e.g., nitrogen-poor soils and low nitrogen fertilizer inputs, which would cause the growth of wild type plants to cease or to be so diminished as to make the wild type plants practically useless. The transgenic plants also can be advantageously used to achieve earlier maturing, faster growing, and/or higher yielding crops and/or produce more nutritious foods and animal feedstocks when cultivated using nitrogen non-limiting growth conditions.

Stacked Traits:

The present invention also encompasses transgenic plants with stacked engineered traits, e.g., a crop having an enhanced phenotype resulting from expression of a trait-improving recombinant DNA, in combination with herbicide and/or pest resistance traits. For example, genes of the current invention can be stacked with other traits of agronomic interest, such as a trait providing herbicide resistance, for example a RoundUp Ready® trait, or insect resistance, such as using a gene from Bacillus thuringensis to provide resistance against lepidopteran, coliopteran, homopteran, hemiopteran, and other insects. Herbicides for which resistance is useful in a plant include glyphosate herbicides, phosphinothricin herbicides, oxynil herbicides, imidazolinone herbicides, dinitroaniline herbicides, pyridine herbicides, sulfonylurea herbicides, bialaphos herbicides, sulfonamide herbicides and gluphosinate herbicides. To illustrate that the production of transgenic plants with herbicide resistance is a capability of those of ordinary skill in the art, reference is made to U.S. patent application publications 2003/0106096A1 and 2002/0112260A1 and U.S. Pat. Nos. 5,034,322; 5,776,760, 6,107,549 and 6,376,754, all of which are incorporated herein by reference. To illustrate that the production of transgenic plants with pest resistance is a capability of those of ordinary skill in the art, reference is made to U.S. Pat. Nos. 5,250,515 and 5,880,275 which disclose plants expressing an endotoxin of Bacillus thuringiensis bacteria, to U.S. Pat. No. 6,506,599 which discloses control of invertebrates which feed on transgenic plants which express dsRNA for suppressing a target gene in the invertebrate, to U.S. Pat. No. 5,986,175 which discloses the control of viral pests by transgenic plants which express viral replicase, and to U.S. Patent Application Publication 2003/0150017 A1 which discloses control of pests by a transgenic plant which express a dsRNA targeted to suppressing a gene in the pest, all of which are incorporated herein by reference.

Once one recombinant DNA has been identified as conferring an enhanced trait of interest in transgenic Arabidopsis plants, several methods are available for using the sequence of that recombinant DNA and knowledge about the protein it encodes to identify homologs of that sequence from the same plant or different plant species or other organisms, e.g., bacteria and yeast. Thus, in one aspect, the invention provides methods for identifying a homologous gene with a DNA sequence homologous to any of SEQ ID NO: 1 through SEQ ID NO: 139, or a homologous protein with an amino acid sequence homologous to any of SEQ ID NO: 140 through SEQ ID NO: 278. In another aspect, the present invention provides the protein sequences of identified homologs for a sequence listed as SEQ ID NO: 279 through SEQ ID NO: 6023. In yet another aspect, the present invention also includes linking or associating one or more desired traits, or gene function with a homolog sequence provided herein.

The trait-improving recombinant DNA and methods of using such trait-improving recombinant DNA for generating transgenic plants with enhanced traits provided by the present invention are not limited to any particular plant species. Indeed, the plants according to the present invention can be of any plant species, e.g., can be monocotyledonous or dicotyledonous. In one embodiment, they will be agricultural useful plants, e.g., plants cultivated by man for purposes of food production or technical, particularly industrial applications. Of particular interest in the present invention are corn and soybean plants. The recombinant DNA constructs optimized for soybean transformation and recombinant DNA constructs optimized for corn transformation are provided by the present invention. Other plants of interest in the present invention for production of transgenic plants having enhanced traits include, without limitation, cotton, canola, wheat, sunflower, sorghum, alfalfa, barley, millet, rice, tobacco, fruit and vegetable crops, and turfgrass.

In certain embodiments, the present invention contemplates to use an orthologous gene in generating the transgenic plants with similarly enhanced traits as the transgenic Arabidopsis counterpart. Enhanced physiological properties in transgenic plants of the present invention can be confirmed in responses to stress conditions, for example in assays using imposed stress conditions to detect enhanced responses to drought stress, nitrogen deficiency, cold growing conditions, or alternatively, under naturally present stress conditions, for example under field conditions. Biomass measures can be made on greenhouse or field grown plants and can include such measurements as plant height, stem diameter, root and shoot dry weights, and, for corn plants, ear length and diameter.

Trait data on morphological changes can be collected by visual observation during the process of plant regeneration as well as in regenerated plants transferred to soil. Such trait data includes characteristics such as normal plants, bushy plants, taller plants, thicker stalks, narrow leaves, striped leaves, knotted phenotype, chlorosis, albino, anthocyanin production, or altered tassels, ears or roots. Other enhanced traits can be identified by measurements taken under field conditions, such as days to pollen shed, days to silking, leaf extension rate, chlorophyll content, leaf temperature, stand, seedling vigor, internode length, plant height, leaf number, leaf area, tillering, brace roots, stay green, stalk lodging, root lodging, plant health, barreness/prolificacy, green snap, and pest resistance. In addition, trait characteristics of harvested grain can be confirmed, including number of kernels per row on the ear, number of rows of kernels on the ear, kernel abortion, kernel weight, kernel size, kernel density and physical grain quality.

To confirm hybrid yield in transgenic corn plants expressing genes of the present invention, it can be desirable to test hybrids over multiple years at multiple locations in a geographical location where maize is conventionally grown, e.g., in Iowa, Illinois or other locations in the midwestern United States, under “normal” field conditions as well as under stress conditions, e.g., under drought or population density stress.

Transgenic plants can be used to provide plant parts according to the invention for regeneration or tissue culture of cells or tissues containing the constructs described herein. Plant parts for these purposes can include leaves, stems, roots, flowers, tissues, epicotyl, meristems, hypocotyls, cotyledons, pollen, ovaries, cells and protoplasts, or any other portion of the plant which can be used to regenerate additional transgenic plants, cells, protoplasts or tissue culture. Seeds of transgenic plants are provided by this invention can be used to propagate more plants containing the trait-improving recombinant DNA constructs of this invention. These descendants are intended to be included in the scope of this invention if they contain a trait-improving recombinant DNA construct of this invention, whether or not these plants are selfed or crossed with different varieties of plants.

The various aspects of the invention are illustrated by means of the following examples which are in no way intended to limit the full breath and scope of claims.

EXAMPLES Example 1 Identification of Recombinant DNA that Confers Enhanced Trait(s) to Plants A. Plant Expression Constructs for Arabidopsi Transformation

Each gene of interest was amplified from a genomic or cDNA library using primers specific to sequences upstream and downstream of the coding region. Transformation vectors were prepared to constitutively transcribe DNA in either sense orientation (for enhanced protein expression) or anti-sense orientation (for endogenous gene suppression) under the control of an enhanced Cauliflower Mosaic Virus 35S promoter (U.S. Pat. No. 5,359,142) directly or indirectly (Moore, e.g., PNAS 95:376-381, 1998; Guyer, e.g., Genetics 149: 633-639, 1998; International patent application NO. PCT/EP98/07577). The transformation vectors also contain a bar gene as a selectable marker for resistance to glufosinate herbicide. The transformation of Arabidopsis plants was carried out using the vacuum infiltration method known in the art (Bethtold, e.g., Methods Mol. Biol. 82:259-66, 1998). Seeds harvested from the plants, named as T1 seeds, were subsequently grown in a glufosinate-containing selective medium to select for plants which were actually transformed and which produced T2 transgenic seed.

B. Soil Drought Tolerance Screen

This example describes a soil drought tolerance screen to identify Arabidopsis plants transformed with recombinant DNA that wilt less rapidly and/or produce higher seed yield when grown in soil under drought conditions

T2 seeds were sown in flats filled with Metro/Mix® 200 (The Scotts® Company, USA). Humidity domes were added to each flat and flats were assigned locations and placed in climate-controlled growth chambers. Plants were grown under a temperature regime of 22° C. at day and 20° C. at night, with a photoperiod of 16 hours and average light intensity of 170 μmol/m²/s. After the first true leaves appeared, humidity domes were removed. The plants were sprayed with glufosinate herbicide and put back in the growth chamber for 3 additional days. Flats were watered for 1 hour the week following the herbicide treatment. Watering was continued every seven days until the flower bud primordia became apparent, at which time plants were watered for the last time.

To identify drought tolerant plants, plants were evaluated for wilting response and seed yield. Beginning ten days after the last watering, plants were examined daily until 4 plants/line had wilted. In the next six days, plants were monitored for wilting response. Five drought scores were assigned according to the visual inspection of the phenotypes: 1 for healthy, 2 for dark green, 3 for wilting, 4 severe wilting, and 5 for dead. A score of 3 or higher was considered as wilted.

At the end of this assay, seed yield measured as seed weight per plant under the drought condition was characterized for the transgenic plants and their controls and analyzed as a quantitative response according to example 1M.

Two approaches were used for statistical analysis on the wilting response. First, the risk score was analyzed for wilting phenotype and treated as a qualitative response according to the example 1L. Alternatively, the survival analysis was carried out in which the proportions of wilted and non-wilted transgenic and control plants were compared over each of the six days under scoring and an overall log rank test was performed to compare the two survival curves using S-PLUS statistical software (S-PLUS 6. Guide to statistics, Insightful. Seattle, Wash., USA). A list of recombinant DNA constructs which improve drought tolerance in transgenic plants is illustrated in Table 4

TABLE 4 NUC PEP Drought score Seed yield SEQ SEQ Construct Nomination Delta Delta ID ID ID ID Orientation mean P-value mean P-value 15 154 17491 CGPG2639 SENSE 0.437 0.006 −1.429 0.021 32 171 18504 CGPG2935 SENSE 0.150 0.233 −0.598 0.013 29 168 19640 CGPG2805 SENSE −0.282 0.027 0.287 0.019 91 230 19869 CGPG4166 SENSE −0.076 0.292 −0.489 0.023 30 169 71530 CGPG2811 SENSE 0.000 0.242 −0.574 0.008 109 248 74307 CGPG5422 SENSE 0.276 0.027 −1.258 0.015 130 269 75611 CGPG7840 SENSE 0.330 0.030 −1.029 0.070 118 257 77801 CGPG7378 SENSE 0.032 0.361 −0.912 0.021

Transgenic plants comprising recombinant DNA expressing protein as set forth in SEQ ID NO: 160, 161, 184, 239, 240 or 268 showed enhanced drought tolerance by the second criteria as illustrated in Example 1L.

C. Heat Stress Tolerance Screen

Under high temperatures, Arabidopsis seedlings become chlorotic and root growth is inhibited. This example sets forth the heat stress tolerance screen to identify Arabidopsis plants transformed with the gene of interest that are more resistant to heat stress based on primarily their seedling weight and root growth under high temperature.

T2 seeds were plated on ½×MS salts, 1/% phytagel, with 10 μg/ml BASTA (7 per plate with 2 control seeds; 9 seeds total per plate). Plates were placed at 4° C. for 3 days to stratify seeds. Plates were then incubated at room temperature for 3 hours and then held vertically for 11 additional days at temperature of 34° C. at day and 20° C. at night. Photoperiod was 16 h. Average light intensity was −140 μmol/m²/s. After 14 days of growth, plants were scored for glufosinate resistance, root length, final growth stage, visual color, and seedling fresh weight. A photograph of the whole plate was taken on day 14.

The seedling weight and root length were analyzed as quantitative responses according to example 1M. The final grow stage at day 14 was scored as success if 50% of the plants had reached 3 rosette leaves and size of leaves are greater than 1 mm (Boyes, et al. (2001) The Plant Cell 13, 1499-1510). The growth stage data was analyzed as a qualitative response according to example 1L. A list of recombinant DNA constructs that improve heat tolerance in transgenic plants illustrated in Table 5.

TABLE 5 Growth stage Root length at day 14 Seedling NUC PEP Con- day 14 Risk weight Seq SEQ struct Delta P- score P- Delta ID ID ID mean value mean value mean P-value 1 140 12796 0.029 0.808 −0.137 0.383 0.783 0.007 31 170 17832 0.311 0.157 0.385 0.235 1.029 0.013 43 182 18240 0.098 0.585 0.095 0.795 0.856 0.021 48 187 18325 −0.001 0.993 0.691 0.085 0.724 0.017 54 193 18436 0.208 0.016 0.548 0.364 1.091 0.009 33 172 18547 0.249 0.230 −0.004 0.918 0.024 34 173 18548 −0.017 0.305 0.525 0.014 0.670 0.038 39 178 18549 0.127 0.441 0.601 0.202 0.912 0.016 57 196 18610 0.093 0.762 0.034 0.586 0.977 0.015 51 190 18843 0.147 0.087 0.603 0.042 0.641 0.006 16 155 19152 0.218 0.183 0.000 0.935 0.004 46 185 19186 0.081 0.586 −0.055 0.645 0.020 29 168 19640 0.070 0.518 0.043 0.762 0.815 0.014 41 180 19644 0.226 0.139 1.126 0.086 1.244 0.003 53 192 19650 −0.182 0.011 −0.062 0.714 0.606 0.008 87 226 19748 0.612 0.016 0.795 0.254 1.149 0.003 84 223 19896 0.172 0.057 0.136 0.269 0.969 0.002 82 221 19920 0.189 0.414 0.993 0.152 1.023 0.017 92 231 19924 0.032 0.455 0.110 0.323 0.877 0.002 81 220 19972 0.136 0.079 1.169 0.001 0.970 0.012 63 202 70452 −0.043 0.557 0.326 0.372 0.735 0.002 65 204 70455 −0.012 0.920 −0.023 0.772 0.506 0.003 61 200 70461 0.295 0.014 1.656 0.121 1.139 0.000 62 201 70470 −0.122 0.507 0.125 0.663 0.783 0.003 64 203 70473 −0.085 0.499 −0.022 0.613 0.676 0.015 70 209 70481 0.179 0.299 −0.018 1.124 0.026 75 214 70483 0.014 0.842 0.914 0.312 0.843 0.018 73 212 70485 0.226 0.314 1.242 0.220 1.339 0.024 66 205 70542 0.139 0.018 0.639 0.527 0.887 0.030 69 208 70546 −0.065 0.712 0.579 0.591 0.780 0.023 76 215 70625 −0.104 0.274 0.466 0.244 0.682 0.004 88 227 70930 0.147 0.322 1.129 0.130 1.044 0.025 30 169 71530 0.100 0.445 −0.107 0.058 0.690 0.021 93 232 71822 0.111 0.458 1.305 0.204 1.139 0.002 107 246 72109 0.101 0.637 −0.007 0.901 1.006 0.012 108 247 72129 0.204 0.202 0.234 0.410 1.189 0.022 23 162 72674 0.145 0.103 0.196 0.693 0.956 0.006 72 211 72907 0.345 0.069 0.901 0.228 1.374 0.005 38 177 73821 −0.078 0.622 −0.151 0.467 0.000 132 271 73934 0.109 0.337 0.239 0.491 1.150 0.012 37 176 74056 0.136 0.335 −0.012 0.816 0.012 14 153 76106 0.221 0.291 0.934 0.218 0.994 0.019 71 210 78318 0.079 0.438 −0.012 0.949 0.905 0.002 139 278 78560 0.204 0.033 0.590 0.260 0.903 0.041 138 277 78989 0.102 0.417 0.308 0.303 0.625 0.014

Transgenic plants comprising recombinant DNA expressing protein as set forth in SEQ ID NO: 179, 222 or 243 showed enhanced heat stress tolerance by the second criteria as illustrated in Example 1L and 1M.

D. Salt Stress Tolerance Screen

This example sets forth the high salinity stress screen to identify Arabidopsis plants transformed with the gene of interest that are tolerant to high levels of salt based on their rate of development, root growth and chlorophyll accumulation under high salt conditions.

T2 seeds were plated on glufosinate selection plates containing 90 mM NaCl and grown under standard light and temperature conditions. All seedlings used in the embodiments were grown at a temperature of 22° C. at day and 20° C. at night, a 16-hour photoperiod, an average light intensity of approximately 120 umol/m². On day 11, plants were measured for primary root length. After 3 more days of growth (day 14), plants were scored for transgenic status, primary root length, growth stage, visual color, and the seedlings were pooled for fresh weight measurement. A photograph of the whole plate was also taken on day 14.

The seedling weight and root length were analyzed as quantitative responses according to example 1M. The final growth stage at day 14 was scored as success if 50% of the plants reached 3 rosette leaves and size of leaves are greater than 1 mm (Boyes, D. C., et al., (2001), The Plant Cell 13, 1499/1510). The growth stage data was analyzed as a qualitative response according to example 1L. A list of recombinant DNA constructs that improve high salinity tolerance in transgenic plants illustrated in Table 6.

TABLE 6 Root Root Growth Seedling NUC length length stage at weight Seq PEP at day 11 at day 14 day 14 at day 14 ID SEQ Delta P- Delta P- Delta P- Delta P- No. ID mean value mean value mean value mean value 52 191 0.351 0.028 0.370 0.014 0.883 0.272 0.878 0.020

Transgenic plants comprising recombinant DNA expressing protein as set forth in SEQ ID NO: 143, 144, 146, 150, 163, 165, 166, 174, 183, 199, 235, 264 or 273 showed enhanced salt stress tolerance by the second criteria as illustrated in Example 1L and 1M.

E. Polyethylene Glycol (PEG) Induced Osmotic Stress Tolerance Screen

There are numerous factors, which can influence seed germination and subsequent seedling growth, one being the availability of water. Genes, which can directly affect the success rate of germination and early seedling growth, are potentially useful agronomic traits for improving the germination and growth of crop plants under drought stress. In this assay, PEG was used to induce osmotic stress on germinating transgenic lines of Arabidopsis thaliana seeds in order to screen for osmotically resistant seed lines.

T2 seeds were plated on BASTA selection plates containing 3% PEG and grown under standard light and temperature conditions. Seeds were plated on each plate containing 3% PEG, ½×MS salts, 1% phytagel, and 10 μg/ml glufosinate. Plates were placed at 4° C. for 3 days to stratify seeds. On day 11, plants were measured for primary root length. After 3 more days of growth, i.e., at day 14, plants were scored for transgenic status, primary root length, growth stage, visual color, and the seedlings were pooled for fresh weight measurement. A photograph of the whole plate was taken on day 14.

Seedling weight and root length were analyzed as quantitative responses according to example 1M. The final growth stage at day 14 was scored as success or failure based on whether the plants reached 3 rosette leaves and size of leaves are greater than 1 mm. The growth stage data was analyzed as a qualitative response according to example 1L. A list of recombinant DNA constructs that improve osmotic stress tolerance in transgenic plants illustrated in Table 7.

TABLE 7 Root Root Growth Seedling length at length at stage weight at day PEP day 11 day 14 at day 14 14 Nuc SEQ Construct Delta P- Delta P- Delta P- Delta SEQ ID ID ID mean value mean value mean value mean P-value 9 148 17523 0.342 0.005 0.283 0.045 2.877 0.124 0.405 0.119 96 235 75032 0.449 0.031 0.545 0.042 1.022 0.581 0.327 0.118

Transgenic plants comprising recombinant DNA expressing protein as set forth in SEQ ID NO: 147, 157, 198, 202, 207, 211, 252, 253, 266 or 272 showed enhanced PEG osmotic stress tolerance by the second criteria as illustrated in Example 1L and 1M.

F. Cold Shock Tolerance Screen

This example set forth a screen to identify Arabidopsis plants transformed with the genes of interest that are more tolerant to cold stress subjected during day 8 to day 28 after seed planting. During these crucial early stages, seedling growth and leaf area increase were measured to assess tolerance when Arabidopsis seedlings were exposed to low temperatures. Using this screen, genetic alterations can be found that enable plants to germinate and grow better than wild type plants under sudden exposure to low temperatures.

Eleven seedlings from T2 seeds of each transgenic line plus one control line were plated together on a plate containing ½×Gamborg Salts with 0.8 Phytagel™, 1% Phytagel, and 0.3% Sucrose. Plates were then oriented horizontally and stratified for three days at 4° C. At day three, plates were removed from stratification and exposed to standard conditions (16 hr photoperiod, 22° C. at day and 20° C. at night) until day 8. At day eight, plates were removed from standard conditions and exposed to cold shock conditions (24 hr photoperiod, 8° C. at both day and night) until the final day of the assay, i.e., day 28. Rosette areas were measured at day 8 and day 28, which were analyzed as quantitative responses according to example 1M. A list of recombinant nucleotides that improve cold shock stress tolerance in plants is illustrated in Table 8.

TABLE 8 Rosette area Rosette area at day 28 Rosette area NUC at day 8 Risk difference Seq ID PEP Delta score Delta No. SEQ ID Construct ID mean P-value mean P-value mean P-value 111 250 12179 −0.611 0.0161 0.0353 0.666 0.862 0.007 36 175 18542 0.583 0.184 0.094 0.019 0.078 0.006 33 172 18547 −0.162 0.531 0.521 0.059 0.622 0.020 51 190 18843 0.114 0.495 0.728 0.009 0.667 0.007 90 229 19796 0.157 0.0886 0.438 0.005 0.382 0.0164 77 216 70489 0.488 0.081 0.312 0.010 0.220 0.311 19 158 70736 −0.213 0.549 0.389 0.013 0.226 0.344 100 239 73675 0.088 0.832 0.586 0.041 0.720 0.032 131 270 75751 0.199 0.251 0.987 0.033 1.093 0.033 20 159 76073 0.510 0.329 0.515 0.020 0.566 0.067

transgenic plants comprising recombinant DNA expressing protein as set forth in PEP SEQ ID NO. 265 or 270 showed enhanced cold stress tolerance by the second criterial as illustrated in Example 1L and 1M.

G. Cold Germination Tolerance Screen

This example sets forth a screen to identify Arabidopsis plants transformed with the genes of interests are resistant to cold stress based on their rate of development, root growth and chlorophyll accumulation under low temperature conditions.

T2 seeds were plated and all seedlings used in the embodiments were grown at 8° C. Seeds were first surface disinfected using chlorine gas and then seeded on assay plates containing an aqueous solution of ½×Gamborg's B/5 Basal Salt Mixture (Sigma/Aldrich Corp., St. Louis, Mo., USA G/5788), 1% Phytagel™ (Sigma-Aldrich, P-8169), and 10 ug/ml glufosinate with the final pH adjusted to 5.8 using KOH. Test plates were held vertically for 28 days at a constant temperature of 8° C., a photoperiod of 16 hr, and average light intensity of approximately 100 umol/m²/s. At 28 days post plating, root length was measured, growth stage was observed, the visual color was assessed, and a whole plate photograph was taken.

The root length at day 28 was analyzed as a quantitative response according to example 1M. The growth stage at day 7 was analyzed as a qualitative response according to example 1L. A list of recombinant DNA constructs that improve cold stress tolerance in transgenic plants illustrated in Table 9.

TABLE 9 Root length Growth stage NUC at day 28 at day 28 Seq ID PEP Construct Nomination Delta P- Delta P- No. SEQ ID ID ID Orientation mean value mean value 43 182 18240 CGPG3289 SENSE 0.289 0.020 0.325 0.029 57 196 18610 CGPG3505 SENSE 0.642 0.059 0.983 0.006 65 204 70455 CGPG3810 SENSE 4.000 73 212 70485 CGPG3857 SENSE 0.213 0.102 0.959 0.010 74 213 70486 CGPG3858 SENSE 0.383 0.223 1.682 0.049 98 237 70773 CGPG4632 SENSE 0.134 0.186 1.455 0.005 89 228 70983 CGPG4112 SENSE 0.362 0.015 2.033 0.059 124 263 75531 CGPG7714 SENSE 0.035 0.778 1.717 0.001 127 266 75572 CGPG7757 SENSE 0.278 0.025 2.252 0.002

Transgenic plants comprising recombinant DNA expressing protein as set forth in SEQ ID NO: 173, 204, 207, 208, 209, 213, 228 or 251 showed enhanced cold stress tolerance by the 10 second criterial as illustrated in Example 1L and 1M.

H. Shade Tolerance Screen

Plants undergo a characteristic morphological response in shade that includes the elongation of the petiole, a change in the leaf angle, and a reduction in chlorophyll content. While these changes can confer a competitive advantage to individuals, in a monoculture the shade avoidance response is thought to reduce the overall biomass of the population. Thus, genetic alterations that prevent the shade avoidance response can be associated with higher yields. Genes that favor growth under low light conditions can also promote yield, as inadequate light levels frequently limit yield. This protocol describes a screen to look for Arabidopsis plants that show an attenuated shade avoidance response and/or grow better than control plants under low light intensity. Of particular interest, we were looking for plants that didn't extend their petiole length, had an increase in seedling weight relative to the reference and had leaves that were more close to parallel with the plate surface.

T2 seeds were plated on glufosinate selection plates with ½ MS medium. Seeds were sown on ½×MS salts, 1% Phytagel, 10 ug/ml BASTA. Plants were grown on vertical plates at a temperature of 22° C. at day, 20° C. at night and under low light (approximately 30 uE/m²/s, far/red ratio (655/665/725/735) ˜0.35 using PLAQ lights with GAM color filter #680). Twenty-three days after seedlings were sown, measurements were recorded including seedling status, number of rosette leaves, status of flower bud, petiole leaf angle, petiole length, and pooled fresh weights. A digital image of the whole plate was taken on the measurement day. Seedling weight and petiole length were analyzed as quantitative responses according to example 1M. The number of rosette leaves, flowering bud formation and leaf angel were analyzed as qualitative responses according to example 1L.

A list of recombinant DNA constructs that improve shade tolerance in plants illustrated in Table 10.

TABLE 10 Seedling weight at Petiole length NUC PEP Con- day 23 at day 23 Scq SEQ struct Nomination Orien- Delta P- Delta P- ID ID ID ID tation mean value mean value  6 145 17507 CGPG2551 SENSE 0.467 0.025 0.312 0.067 84 223 19896 CGPG4015 SENSE 0.360 0.035 0.262 0.060 99 238 70215 CGPG490 SENSE −0.080 0.133 −0.088 0.050

For “seeding weight”, if p<0.05 and delta or risk score mean>0, the transgenic plants showed statistically significant trait enhancement as compared to the reference. If p<0.2 and delta or risk score mean>0, the transgenic plants showed a trend of trait enhancement as compared to the reference with p<0.2.

For “petiole length”, if p<0.05 and delta <0, the transgenic plants showed statistically significant trait enhancement as compared to the reference. If p<0.2 and delta <0, the transgenic plants showed a trend of trait enhancement as compared to the reference.

Transgenic plants comprising recombinant DNA expressing protein as set forth in SEQ ID NO: 160, 184, 197, 225, 233, 234, 236, 237, 241, 242, 255, 258, 259, 260, 263, 267 or 276 showed enhanced tolerance to shade or low light condition by the second criterial as illustrated in Example 1L and 1M.

I. Early Plant Growth and Development Screen

This example sets forth a plate based phenotypic analysis platform for the rapid detection of phenotypes that are evident during the first two weeks of growth. In this screen, we were looking for genes that confer advantages in the processes of germination, seedling vigor, root growth and root morphology under non-stressed growth conditions to plants. The transgenic plants with advantages in seedling growth and development were determined by the seedling weight and root length at day 14 after seed planting.

T2 seeds were plated on glufosinate selection plates and grown under standard conditions (˜100 uE/m² is, 16 h photoperiod, 22° C. at day, 20° C. at night). Seeds were stratified for 3 days at 4° C. Seedlings were grown vertically (at a temperature of 22° C. at day 20° C. at night). Observations were taken on day 10 and day 14. Both seedling weight and root length at day 14 were analyzed as quantitative responses according to example 1M.

A list recombinant DNA constructs that improve early plant growth and development illustrated in Table 11.

TABLE 11 Seedling Root length Root length weight NUC PEP Con- at day 10 at day 14 at day 14 Seq SEQ struct Delta P- Delta P- Delta ID ID ID mean value mean value mean P-value 8 147 17521 0.508 0.003 0.385 0.003 0.164 0.222 17 156 17907 0.588 0.021 25 164 17911 0.272 0.049 0.107 0.295 0.254 0.091 50 189 18248 0.477 0.014 0.301 0.004 0.592 0.048 2 141 18301 0.200 0.173 0.157 0.048 0.299 0.001 42 181 18836 0.081 0.426 0.144 0.037 0.066 0.734 80 219 19880 0.405 0.010 0.239 0.003 0.459 0.024 85 224 19957 0.234 0.052 0.240 0.035 0.332 0.027 110 249 72926 0.244 0.024 0.119 0.304 0.235 0.033 78 217 74202 0.094 0.044 0.080 0.056 0.025 0.587 28 167 78468 0.194 0.050 0.087 0.039 0.309 0.039 90 229 19796 0.274 0.004 0.221 0.022 0.561 0.0002

Transgenic plants comprising recombinant DNA expressing a protein as set forth in SEQ ID NO: 149, 155, 165, 173, 174, 186, 218 or 243 showed enhanced tolerance to shade or low light condition by the second criterial as illustrated in Example 1L and 1M.

J. Late Plant Growth and Development Screen

This example sets forth a soil based phenotypic platform to identify genes that confer advantages in the processes of leaf development, flowering production and seed maturity to plants.

Arabidopsis plants were grown on a commercial potting mixture (Metro Mix 360, Scotts Co., Marysville, Ohio) consisting of 30-40% medium grade horticultural vermiculite, 35-55% sphagnum peat moss, 10-20% processed bark ash, 1-15% pine bark and a starter nutrient charge. Soil was supplemented with Osmocote time-release fertilizer at a rate of 30 mg/ft³. T2 seeds were imbibed in 1% agarose solution for 3 days at 4° C. and then sown at a density of ˜5 per ½″ pot. Thirty-two pots were ordered in a 4 by 8 grid in standard greenhouse flat. Plants were grown in environmentally controlled rooms under a 16 h day length with an average light intensity of ˜200 μmoles/m²/s. Day and night temperature set points were 22° C. and 20° C., respectively. Humidity was maintained at 65%. Plants were watered by sub-irrigation every two days on average until mid-flowering, at which point the plants were watered daily until flowering was complete.

Application of the herbicide glufosinate was performed to select T2 individuals containing the target transgene. A single application of glufosinate was applied when the first true leaves were visible. Each pot was thinned to leave a single glufosinate-resistant seedling ˜3 days after the selection was applied.

The rosette radius was measured at day 25. The silique length was measured at day 40. The plant parts were harvested at day 49 for dry weight measurements if flowering production was stopped. Otherwise, the dry weights of rosette and silique were carried out at day 53. The seeds were harvested at day 58. All measurements were analyzed as quantitative responses according to example 1M.

A list of recombinant DNA constructs that improve late plant growth and development illustrated in Table 12.

TABLE 12 Rosette dry Rosette Seed net dry Silique dry weight at radius weight at weight at Silique length NUC PEP day 53 at day 25 day 62 day 53 at day 40 SEQ SEQ Delta P- Delta Delta P- Delta P- Delta P- ID ID mean value mean P-value mean value mean value mean value 17 156 −0.333 0.026 0.000 1.000 1.401 0.017 0.419 0.040 0.020 0.635 61 200 −0.354 0.147 −0.120 0.139 1.079 0.006 0.009 0.819 3 142 −0.234 0.138 −0.024 0.756 1.618 0.000 −0.192 0.476 0.025 0.100 123 262 −0.057 0.586 0.042 0.480 0.985 0.014 −0.085 0.537 −0.068 0.363

If p<0.05 and delta or risk score mean>0, the transgenic plants showed statistically significant trait enhancement as compared to the reference. If p<0.2 and delta or risk score mean>0, the transgenic plants showed a trend of trait enhancement as compared to the reference. Transgenic plants comprising recombinant DNA expressing protein as set forth in SEQ ID NO: 245 showed enhanced tolerance to shade or low light condition by the second criterial as illustrated in Example 1L and 1M.

K. Limited Nitrogen Tolerance Screen

Under low nitrogen conditions, Arabidopsis seedlings become chlorotic and have less biomass. This example sets forth the limited nitrogen tolerance screen to identify Arabidopsis plants transformed with the gene of interest that are altered in their ability to accumulate biomass and/or retain chlorophyll under low nitrogen condition.

T2 seeds were plated on glufosinate selection plates containing 0.5× N-Free Hoagland's T 0.1 mM NH₄NO₃ T 0.1% sucrose T 1% phytagel media and grown under standard light and temperature conditions. At 12 days of growth, plants were scored for seedling status (i.e., viable or non-viable) and root length. After 21 days of growth, plants were scored for BASTA resistance, visual color, seedling weight, number of green leaves, number of rosette leaves, root length and formation of flowering buds. A photograph of each plant was also taken at this time point.

The seedling weight and root length were analyzed as quantitative responses according to example 1M. The number green leaves, the number of rosette leaves and the flowerbud formation were analyzed as qualitative responses according to example 1L. The leaf color raw data were collected on each plant as the percentages of five color elements (Green, DarkGreen, LightGreen, RedPurple, YellowChlorotic) using a computer imaging system. A statistical logistic regression model was developed to predict an overall value based on five colors for each plant.

A list of recombinant DNA constructs that improve low nitrogen availability tolerance in plants illustrated in Table 13.

TABLE 13 Leaf color at day 21 Rosette weight NUC Risk at day 21 SEQ PEP Construct Nomination score P- Delta P- ID SEQ ID ID ID Orientation mean value mean value 136 275 10804 CGPG477 ANTI- 3.281 0.015 −0.118 0.063 SENSE 55 194 19634 CGPG3468 SENSE 1.332 0.025 −0.008 0.933 79 218 71971 CGPG3879 SENSE 1.566 0.539 0.182 0.011 105 244 72117 CGPG5316 SENSE −1.264 0.178 0.060 0.048 106 245 72118 CGPG5324 SENSE 2.897 0.130 0.093 0.018 104 243 72106 CGPG5306 SENSE −1.867 0.048 0.117 0.018 125 264 75594 CGPG7743 SENSE −4.165 0.0009 −0.216 0.344

For rosette weight, if p<0.05 and delta or risk score mean>0, the transgenic plants showed statistically significant trait enhancement as compared to the reference. If p<0.2 and delta or risk score mean>0, the transgenic plants showed a trend of trait enhancement as compared to the reference with p<0.2. For root length, if p<0.05, the transgenic plants showed statistically significant trait enhancement as compared to the reference. If p<0.2, the transgenic plants showed a trend of trait enhancement as compared to the reference.

Transgenic plants comprising recombinant DNA expressing a protein as set forth in SED ID NO: 151, 152, 188, 195, 206, 254, 256, 261, 264, or 274 showed enhanced tolerance to shade or low light condition by the second criterial as illustrated in Example 1L and 1M.

L. Statistic Analysis for Qualitative Responses

A list of responses that were analyzed as qualitative responses illustrated in Table 14.

TABLE 14 categories response Screen (success vs. failure) Wilting response Soil drought non-wilted vs. wilted Risk Score tolerance screen growth stage at heat stress 50% of plants reach day 14 tolerance screen stage1.03 vs. not growth stage at salt stress 50% of plants reach day 14 tolerance screen stage1.03 vs. not growth stage at PEG induced 50% of plants reach day 14 osmotic stress stage1.03 vs. not tolerance screen growth stage at cold germination 50% of plants reach day 7 tolerance screen stage 0.5 vs. not number of rosette Shade tolerance 5 leaves appeared vs. leaves at day 23 screen not Flower bud Shade tolerance flower buds appear vs. formation at screen not day 23 leaf angle at Shade tolerance >60 degree vs. <60 day 23 screen degree number of green limited nitrogen 6 or 7 leaves appeared leaves at day 21 tolerance screen vs. not number of rosette limited nitrogen 6 or 7 leaves appeared leaves at day 21 tolerance screen vs. not Flower bud limited nitrogen flower buds appear vs. formation at tolerance screen not day 21

Plants were grouped into transgenic and reference groups and were scored as success or failure according to Table 14. First, the risk (R) was calculated, which is the proportion of plants that were scored as of failure plants within the group. Then the relative risk (RR) was calculated as the ratio of R (transgenic) to R (reference). Risk score (RS) was calculated as −log₂ ^(RR). Two criteria were used to determine a transgenic with enhanced trait(s). Transgenic plants comprising recombinant DNA disclosed herein showed trait enhancement according to either or both of the two criteria.

For the first criteria, the risk scores from multiple events of the transgene of interest were evaluated for statistical significance by t-test using SAS statistical software (SAS 9, SAS/STAT User's Guide, SAS Institute Inc., Cary, N.C., USA). RS with a value greater than 0 indicates that the transgenic plants perform better than the reference. RS with a value less than 0 indicates that the transgenic plants perform worse than the reference. The RS with a value equal to 0 indicates that the performance of the transgenic plants and the reference don't show any difference. If p<0.05 and risk score mean>0, the transgenic plants showed statistically significant trait enhancement as compared to the reference. If p<0.2 and risk score mean>0, the transgenic plants showed a trend of trait enhancement as compared to the reference.

For the second criteria, the RS from each event was evaluated for statistical significance by t-test using SAS statistical software (SAS 9, SAS/STAT User's Guide, SAS Institute Inc, Cary, N.C., USA). The RS with a value greater than 0 indicates that the transgenic plants from this event performs better than the reference. The RS with a value less than 0 indicates that the transgenic plants from this event perform worse than the reference. The RS with a value equal to 0 indicates that the performance of the transgenic plants from this event and the reference don't show any difference. If p<0.05 and risk score mean>0, the transgenic plants from this event showed statistically significant trait enhancement as compared to the reference. If p<0.2 and risk score mean>0, the transgenic plants showed a trend of trait enhancement as compared to the reference. If two or more events of the transgene of interest showed improvement in the same response, the transgene was deemed to show trait enhancement.

M. Statistic Analysis for Quantitative Responses

A list of responses that were analyzed as quantitative responses illustrated in Table 15.

TABLE 15 response screen seed yield Soil drought stress tolerance screen seedling weight at day 14 heat stress tolerance screen root length at day 14 heat stress tolerance screen seedling weight at day 14 salt stress tolerance screen root length at day 14 salt stress tolerance screen root length at day 11 salt stress tolerance screen seedling weight at day 14 PEG induced osmotic stress tolerance screen root length at day 11 PEG induced osmotic stress tolerance screen root length at day 14 PEG induced osmotic stress tolerance screen rosette area at day 8 cold shock tolerance screen rosette area at day 28 cold shock tolerance screen difference in rosette area cold shock tolerance screen from day 8 to day 28 root length at day 28 cold germination tolerance screen seedling weight at day 23 Shade tolerance screen petiole length at day 23 Shade tolerance screen root length at day 14 Early plant growth and development screen Seedling weight at day14 Early plant growth and development screen Rosette dry weight at day 53 Late plant growth and development screen rosette radius at day 25 Late plant growth and development screen seed dry weight at day 58 Late plant growth and development screen silique dry weight at day 53 Late plant growth and development screen silique length at day 40 Late plant growth and development screen Seedling weight at day 21 Limited nitrogen tolerance screen Root length at day 21 Limited nitrogen tolerance screen

The measurements (M) of each plant were transformed by log₂ calculation. The Delta was calculated as log₂M(transgenic)−log₂M(reference). Two criteria were used to determine trait enhancement. A transgene of interest could show trait enhancement according to either or both of the two criteria. The measurements (M) of each plant were transformed by log₂ calculation. The Delta was calculated as log₂M(transgenic)−log₂M(reference). If the measured response was Petiole Length for the Low Light assay, Delta was subsequently multiplied by −1, to account for the fact that a shorter petiole length is considered an indication of trait enhancement.

For the first criteria, the Deltas from multiple events of the transgene of interest were evaluated for statistical significance by t-test using SAS statistical software (SAS 9, SAS/STAT User's Guide, SAS Institute Inc, Cary, N.C., USA). Delta with a value greater than 0 indicates that the transgenic plants perform better than the reference. Delta with a value less than 0 indicates that the transgenic plants perform worse than the reference. The Delta with a value equal to 0 indicates that the performance of the transgenic plants and the reference don't show any difference. If p<0.05 and risk score mean>0, the transgenic plants showed statistically significant trail enhancement as compared to the reference. If p<0.2 and risk score mean>0, the transgenic plants showed a trend of trait enhancement as compared to the reference.

For the second criteria, the delta from each event was evaluated for statistical significance by t-test using SAS statistical software (SAS 9, SAS/STAT User's Guide, SAS Institute Inc., Cary, N.C., USA). The Delta with a value greater than 0 indicates that the transgenic plants from this event performs better than the reference. The Delta with a value less than 0 indicates that the transgenic plants from this event perform worse than the reference. The Delta with a value equal to 0 indicates that the performance of the transgenic plants from this event and the reference don't show any difference. If p<0.05 and delta mean>0, the transgenic plants from this event showed statistically significant trait improvement as compared to the reference. If p<0.2 and delta mean>0, the transgenic plants showed a trend of trait enhancement as compared to the reference. If two or more events of the transgene of interest showed enhancement in the same response, the transgene was deemed to show trait improvement.

Example 2 Identification of Homologs

A BLAST searchable “All Protein Database” is constructed of known protein sequences using a proprietary sequence database and the National Center for Biotechnology Information (NCBI) non-redundant amino acid database (nr.aa). For each organism from which a DNA sequence provided herein was obtained, an “Organism Protein Database” is constructed of known protein sequences of the organism; the Organism Protein Database is a subset of the All Protein Database based on the NCBI taxonomy ID for the organism.

The All Protein Database is queried using amino acid sequence of protein for gene DNA used in trait-improving recombinant DNA, e.g., sequences of SEQ ID NO: 140 through SEQ ID NO: 278 using “blastp” with E-value cutoff of 1e⁻⁸. Up to 1000 top hits were kept, and separated by organism names. For each organism other than that of the query sequence, a list is kept for hits from the query organism itself with a more significant E-value than the best hit of the organism. The list contains likely duplicated genes, and is referred to as the Core List. Another list was kept for all the hits from each organism, sorted by E-value, and referred to as the Hit List.

The Organism Protein Database is queried using amino acid sequences of SEQ ID NO: 140 through SEQ ID NO: 278 using “blastp” with E-value cutoff of 1e⁻⁴. Up to 1000 top hits are kept. A BLAST searchable database is constructed based on these hits, and is referred to as “SubDB”. SubDB was queried with each sequence in the Hit List using “blastp” with E-value cutoff of 1e⁻⁸. The hit with the best E-value is compared with the Core List from the corresponding organism. The hit is deemed a likely ortholog if it belongs to the Core List, otherwise it is deemed not a likely ortholog and there is no further search of sequences in the Hit List for the same organism. Likely orthologs from a large number of distinct organisms were identified and are reported by amino acid sequences of SEQ ID NO: 279 to SEQ ID NO: 6023. These orthologs are reported in Tables 16 as homologs to the proteins corresponding to genes used in trait-improving recombinant DNA.

TABLE 16 SEQ ID NO: homolog SEQ ID NOs 140 706 583 749 1086 889 4107 4890 5430 5612 5594 5975 5992 3470 3467 4873 5969 2008 1250 2884 2958 5903 2565 2070 1078 773 2235 4335 3214 4415 4455 3698 2745 2621 5012 3281 5559 5099 4670 5882 4112 292 2139 2117 574 3241 5646 765 141 5572 480 2492 5574 3604 3508 1313 4894 2962 1986 980 1872 2159 5857 2531 4416 2195 5995 3011 1037 1829 1932 332 142 1425 4267 1156 1158 3175 3370 5813 5349 323 1183 3689 3801 5576 909 3422 143 1940 1119 2138 1862 5052 5472 868 572 1040 4058 676 5951 1286 4676 5427 5999 6004 144 4034 1262 5043 4488 3122 382 2293 4246 5255 3244 265 2807 2929 5984 4993 1551 4627 1294 1566 1459 458 4519 2776 1652 2082 2649 5796 2283 2023 4293 4315 1293 4100 3901 3311 4688 4068 820 1612 1221 4055 3085 1996 4893 3751 5025 2729 845 2135 3195 3814 4466 5641 5108 5763 2640 586 4810 5694 4552 496 1055 1714 4402 1493 3104 145 4559 4904 5098 4982 1325 2232 4706 2837 146 4044 4599 4596 4123 4126 4927 3191 3185 3187 1517 523 421 469 474 3181 3946 3466 1289 684 2433 4760 554 5051 1173 1177 4119 4157 4154 4153 1653 1623 4318 3119 1096 1895 1538 686 1291 3891 370 4991 5005 4396 2493 386 3794 1257 5775 2919 1934 5213 4973 1838 3945 5344 5304 2122 4587 646 5819 2977 2759 3349 2817 2736 5208 526 1147 525 551 550 548 547 1144 2160 2158 2163 1561 1801 1804 608 626 4158 2547 1771 1137 1923 751 299 5783 690 1295 5690 3430 833 992 1100 4289 1726 5130 3169 3149 582 3850 147 2968 1281 3943 3942 2774 2848 2846 3813 1113 1696 1881 1858 5614 1426 1427 1900 1902 1879 1876 1057 3093 2526 2530 2522 1823 1821 4989 2826 2824 2026 2027 4260 5513 5078 2002 4849 3096 3094 1850 1848 2532 1851 1056 1700 1633 2879 1017 3441 3443 3884 2057 2054 2024 2000 1997 1781 2494 1110 2855 1115 5275 2020 402 4915 2190 1957 931 2654 4159 4332 5767 1062 1061 1085 1083 2489 1087 1673 1698 3188 1815 1713 3439 4122 3541 5209 2025 1386 1363 1391 3739 3815 4065 5795 1865 4640 4278 2787 2984 2735 5981 1990 1972 1974 1646 2858 1600 1596 2225 2204 2211 1595 2208 2227 2199 2223 2224 2202 1114 1116 738 367 5838 4568 647 450 5010 2251 5512 2691 1129 2798 641 659 4698 1165 1089 1716 4731 2721 2306 2324 1754 1907 1760 4220 4238 2121 1373 3967 5220 4005 4022 3832 3835 3852 2175 1521 4240 405 1395 4268 1569 516 1752 2019 2073 2074 1689 654 2092 4857 2046 3575 5183 2042 3831 2593 705 3763 3296 5917 5625 2641 5890 2658 1108 4250 3736 2327 3342 374 5119 1079 3170 1813 3859 2820 2080 1039 2497 2500 5121 3783 3803 4103 3382 3385 1976 3336 2313 1311 353 2646 3954 2071 1971 4404 609 1675 1694 3840 4456 1530 4622 1202 3539 2203 148 4182 2778 4726 3323 4652 2981 322 390 3479 1263 2331 1241 1956 5803 3120 4500 4418 732 4740 2645 149 3953 1949 1651 4276 5811 2557 5727 4517 2978 4020 3215 4950 3135 150 2990 2566 3100 4734 3825 756 4214 5757 3851 2321 4679 5525 3354 3855 3941 5018 3517 4172 3250 5399 873 151 2968 2970 4423 3943 3942 1859 5233 1155 3627 3653 4236 4254 3680 4989 3816 2771 3935 5513 5138 3009 5832 5266 3963 3964 3707 3711 2002 4790 5326 5331 5192 3940 3921 3687 305 2329 5540 5724 5235 3556 5395 1633 3784 4113 1017 3884 2024 2057 2000 1997 2923 2855 3489 3490 5198 2186 4613 5382 5392 5387 5887 2051 2020 2021 452 455 2628 476 5122 4332 803 4118 5139 3739 1945 1941 3128 2596 2614 4690 932 910 929 3105 3101 3080 5069 3010 3026 3013 3012 3815 546 5153 2342 2936 2924 5254 5251 3672 4241 4453 3675 4640 5652 1952 1774 2735 1882 3728 3702 3704 591 5231 1990 1972 1974 1646 5408 2612 2642 2699 4985 4841 5637 4876 1114 1116 219 5072 5101 4785 4225 4752 4753 5415 5352 3660 6003 5114 541 5054 5132 3914 3919 3916 1548 3402 902 2721 2718 3334 5965 1543 3087 4523 5088 4134 806 1338 1340 3967 3966 4244 2053 3992 5602 4005 4003 3944 5355 5358 5363 4249 3807 979 981 4497 2877 1581 2340 2050 908 1926 1584 2872 4266 5369 5453 5449 5421 5423 2098 3930 4102 2942 563 2667 2623 1368 4475 4399 911 2345 1964 5889 4704 4192 4008 2686 4811 2806 2939 3636 681 3639 2946 2948 4713 4831 4830 2644 1857 4103 2529 1908 3385 2799 1740 1861 6023 2943 2941 3033 3049 1311 3074 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991 5691 230 1654 1562 2695 2880 655 4394 1611 5197 5721 1822 1816 2069 3853 1296 2458 4683 3699 1159 5124 1690 4210 1819 1810 786 2084 1378 4205 4092 688 714 692 349 5880 231 5343 1525 1526 2766 4432 5952 3051 1603 808 1831 4465 2072 4062 5011 2843 3725 1688 2876 3040 5404 3294 5367 1345 3314 5436 3208 1479 1480 839 5465 2932 3982 3292 3310 3317 2448 2446 670 3498 2930 1472 350 1468 4342 303 4936 4643 3523 5835 2453 5168 5167 5295 4739 5388 746 4253 1364 3209 755 5341 2298 3793 930 2386 2388 3432 1913 1911 5822 587 618 5841 677 710 4732 5825 4735 4725 5338 3035 832 1384 5885 2618 513 2264 3669 1621 2842 1624 4637 777 1528 994 1033 2418 1692 983 2610 976 1465 1554 840 649 5507 5037 3545 4864 232 1411 2629 4051 5110 2437 2843 5160 5759 3410 2662 2875 2617 2687 3638 437 2017 2579 2533 2954 443 466 467 462 1699 4160 313 4017 486 470 369 4708 5953 4957 5586 2281 4164 1592 233 764 3328 3330 1053 1075 2723 2725 1030 1088 2680 5450 5452 5818 5791 5494 5470 5497 5227 4850 4844 4848 2683 3427 1104 2682 2061 1038 3322 3325 4401 488 5282 5362 5359 5365 5274 3779 3713 3663 3569 3635 3661 3560 3633 3666 3565 661 4338 2527 2782 1035 2751 2755 2753 3368 2638 3372 1084 3374 3395 5288 5287 5289 4717 5802 3428 5805 5790 5788 5310 5311 5313 5949 5891 5901 5920 5959 5923 5974 5926 5980 5925 3650 3654 5210 4814 4817 4822 4820 5503 5517 5520 5500 5499 5518 5521 5332 5334 5335 5393 5389 5269 5309 5305 5426 5422 5462 5466 5458 5490 5485 5492 2703 2706 2524 3464 3527 2756 1036 4881 4878 4854 4851 592 4155 3778 3709 3764 2270 4508 4721 4718 5459 5467 5464 4917 4914 5468 4911 529 553 2592 2348 1448 2198 2956 1463 2957 2979 1444 652 4925 1849 4233 1825 5418 5420 3561 4336 3566 3461 5283 4763 4755 4758 4888 4884 4886 3547 2727 3640 3692 5041 4487 3608 4620 3304 4131 3044 4052 3534 3667 3611 3688 3609 4794 4792 4791 4796 4812 4767 4787 5765 4026 3434 4230 4786 4783 4232 4960 2636 1054 2516 3459 3493 3462 4333 955 5034 924 2417 711 885 884 2442 3495 1871 1854 487 506 5563 5593 5582 5510 5538 2959 1077 1106 2436 2422 3491 2472 5053 5750 949 953 3530 3535 5174 2701 5950 5895 5476 5480 1442 1447 3691 3694 3629 3631 3331 1058 2779 2580 2584 1034 2719 3454 1111 2720 3613 3734 3757 3632 3759 3665 4215 4588 4616 4929 4980 4933 2894 2895 5904 5957 4828 5927 5982 3804 3671 867 3062 730 234 2552 2110 3754 2029 5207 3021 1130 3000 2063 1471 2598 3819 235 5202 1642 2809 1617 4111 3024 1002 3715 5955 3589 5971 1575 4300 3290 1893 3628 4308 2162 1222 3761 236 2402 2466 3951 3064 1757 4355 1414 1365 4070 1822 1816 3995 5865 3699 3262 1690 1975 1810 1819 2910 539 866 3882 237 3937 5922 1193 3378 2697 4085 2953 5407 238 3068 1379 2332 745 2292 2818 3258 5265 1374 1209 1944 683 224 2927 2003 1473 430 394 5286 3042 1981 1978 2004 5260 570 2409 3486 3714 2407 1413 4610 5340 5148 1783 2415 5739 3879 3718 4703 1796 1701 3008 2549 1133 5862 4080 2123 3537 4041 1855 542 3697 796 4407 239 819 5267 2716 3929 615 1920 5618 3555 2428 3445 3444 5330 5967 4793 3685 4937 3928 3359 1602 1775 240 1654 4696 1322 5737 1216 1987 2695 3106 655 4394 2792 1334 3153 5294 5107 1769 2368 5386 708 3991 2763 637 5506 5721 1822 1816 5445 2305 5705 2458 4683 3118 3853 1296 2266 3774 939 2099 2097 3699 3716 2413 3993 3065 328 781 2394 5124 1690 2364 584 4040 2379 5778 5564 1819 1810 786 509 688 714 692 349 5880 241 5681 3973 2791 4701 2239 4033 1412 5740 3592 1963 1253 2031 1960 1299 2677 1695 3477 3081 4194 4754 2902 3727 1661 4669 5030 3869 1798 4560 1615 2075 1456 1236 5434 3205 2126 294 1742 4939 5751 5154 296 2793 3553 888 5793 499 2509 638 2898 3863 5276 2242 2544 2572 4746 1809 3796 5575 4222 4593 4932 5412 5149 2125 5264 3433 4446 3594 996 829 242 5416 2359 5038 4784 5152 2568 498 2441 1246 1192 1773 4074 1292 3562 2356 2465 2586 243 4406 4254 4236 1426 1427 3680 4989 2771 2829 5138 3009 5832 5271 5078 5079 5192 3940 3921 3687 305 3278 3275 2329 5540 2878 5724 1839 3556 3784 4113 3884 1997 5736 5666 1781 1779 2923 2821 3489 3490 4613 2186 5275 5887 3488 4388 805 803 5139 3739 1941 1945 3128 3133 3129 910 929 3105 3101 3080 3010 3013 3026 3012 1301 4264 546 5795 5153 1327 1317 2936 2924 4640 1563 2735 1990 1972 1974 5376 4876 4872 738 4261 4225 4752 5142 4243 5114 3055 5054 5132 3919 3914 3916 1548 3402 3076 902 5893 2985 5864 1543 2121 4244 2053 3992 3944 3710 4249 3807 979 981 982 2877 4497 1581 2340 1926 2050 908 1584 3998 2282 2872 4181 1546 4266 5369 2098 2345 1964 2686 5442 2320 4811 2806 2939 871 3859 2948 2946 5064 4713 5929 4451 5956 4831 4830 2644 293 3783 3803 3786 3788 4103 2414 2529 1908 2799 1976 2943 2941 4193 3033 3049 1311 3074 3077 3030 3028 3108 3123 3102 3103 2646 4716 2134 1971 609 2747 611 3840 1993 5196 1530 4781 4245 5732 5158 244 4044 4513 308 3533 2607 974 1836 1071 1069 418 421 3996 2786 3083 3684 5875 4441 4440 4417 4414 2583 2540 2273 3236 3747 5609 3750 2338 4512 316 1662 4124 4129 2651 1542 3887 5685 5684 1257 1443 3735 2635 1665 4452 640 5477 860 2966 2451 5628 896 2762 5171 5654 1715 4504 3475 2427 3132 5263 4097 3939 2975 5546 4369 4234 5213 1934 4372 653 672 1131 3167 2503 2475 2445 3005 5553 1777 5672 3206 1609 3652 4145 5976 1691 4677 6014 2951 3091 4081 3145 3756 1260 3448 2257 4800 1227 1229 1231 4943 4944 3854 436 2868 2808 2246 432 4331 5457 5861 782 784 5113 2815 1919 785 938 511 1120 1524 5022 2016 2335 3985 4027 4459 5806 3399 3283 2874 757 3706 5687 3430 3327 3053 3874 2366 582 5817 5782 245 697 5617 4680 4007 671 942 4312 3383 954 1220 1219 5232 4978 2105 687 2137 1806 3067 3318 3347 695 2400 2421 2705 1240 1242 4645 4650 3997 1235 5212 2118 5531 4185 5001 3957 5046 5048 1768 246 4304 2904 917 1059 2089 5647 318 874 736 855 3356 858 3595 2151 3150 5061 494 2310 3990 3988 1371 300 1374 1797 5169 3977 1210 1998 2390 5562 5558 4086 415 3740 3577 3617 4387 2789 1142 2289 2274 3348 3084 2937 2825 3507 5286 4391 2278 2280 571 331 1381 1022 3722 2473 1793 1772 1703 2145 3833 5935 5118 4949 3838 2961 3151 5674 5189 5567 3625 4473 3099 4458 972 3800 4509 1011 3069 1187 622 673 1102 2548 368 2993 2901 2852 2863 4526 3264 2230 2010 247 2359 5038 4644 1759 5989 644 3904 3906 648 3956 1484 3159 1834 5076 801 4542 565 5007 2459 2101 2425 4305 5049 5150 3573 5015 703 4635 3329 5734 5937 2989 5537 4546 1192 1773 4074 3562 5645 1788 2861 248 2450 409 5292 3436 1514 3766 3765 913 617 5279 1184 2244 4773 1491 4219 1970 3659 5385 4347 5411 326 5086 249 722 2797 484 3115 4998 1669 1392 869 5103 3437 650 4748 5092 5815 2067 907 5194 600 5962 5253 815 1512 691 2095 1553 1557 1550 1552 4296 4099 4343 4217 2511 2796 4550 4191 1936 377 327 2259 1506 4528 3782 4061 5314 2183 4292 5157 823 5571 4469 603 2921 2969 321 1416 250 324 4801 2498 1000 457 987 3532 780 5616 3540 1894 3642 1481 1429 4970 5820 4952 899 3136 5762 5439 4946 4405 5509 552 3512 4837 3862 2393 875 3268 663 2671 2233 1676 1179 251 2353 5695 1795 1794 5504 3843 3220 3837 1335 1723 1046 1933 2769 4922 1290 4340 3798 4518 4647 501 2440 4628 4782 4738 4768 2222 5141 4912 4563 4607 3500 5542 2605 453 2773 1744 5549 3180 3974 4570 5843 2377 5660 2917 3729 4648 3514 3109 1534 4769 2115 2949 1636 798 3041 1656 4707 4098 2974 2197 5454 4840 5595 1743 4700 1666 3174 3536 4412 284 2965 2847 5058 5954 5972 1064 508 5596 2468 5484 2205 4397 3978 5626 2229 1601 2269 2248 5384 5440 252 1727 1725 2767 3365 4273 1103 3421 4764 5964 3273 3341 3338 3949 4586 3089 1101 5094 5892 355 2460 451 2085 2560 2556 3401 3396 1309 1880 2887 3003 3857 1207 5906 5872 5248 2408 2562 4585 3113 3210 2711 1660 2785 425 5599 4187 333 4479 1140 1143 1126 3624 1519 2485 4038 964 3829 2247 253 5244 5284 5184 4859 2375 4221 2154 556 4067 4449 3146 2357 990 4923 3429 5460 2553 5249 2156 5606 2674 3147 1333 5730 5990 4481 1785 5247 5268 2906 2828 2637 5397 1828 5191 3134 3668 2449 2164 5966 5611 2079 2263 1063 2490 1188 1282 2362 741 3251 2250 1802 1223 254 1948 2237 2487 5068 3207 4549 1018 2430 4584 4461 5166 5598 3276 1072 5111 5127 5697 747 4898 1369 634 1558 2922 2240 1811 477 1091 4435 3559 2265 1050 943 3211 1048 2392 2971 3333 2619 3883 4306 2802 3981 5188 5792 5896 5180 4274 4270 5394 814 3686 3948 2272 1523 5700 588 309 2597 2841 413 1734 5749 2909 4228 2905 2908 2903 2891 1889 1973 1455 2940 4499 1866 5898 4001 5707 5580 2142 2882 5488 5678 2258 5627 1498 358 3492 2236 3762 1171 5433 5419 5621 3760 1681 3367 991 4339 255 4044 4513 5002 967 418 3181 4392 3554 2955 2700 2535 316 370 386 1257 2185 1032 1667 1376 2536 2322 2900 5651 5342 2608 5319 4800 410 1804 432 1153 2335 3158 4852 5783 833 992 4503 5817 256 2353 5695 1795 1794 5504 5045 774 3979 5400 5360 2769 4922 475 4299 1375 3798 4518 4647 501 2555 1732 1852 5660 2917 3729 4648 3514 3516 3522 3487 3519 3581 2434 4769 5221 916 5315 5143 5000 490 5605 5134 5302 4885 2176 5201 448 4114 2245 2201 2083 3978 2229 1601 2269 2248 5384 1271 411 3178 5440 977 1230 3773 257 2466 1843 1846 4582 1562 4137 4141 4133 4108 3552 1756 4377 1822 1816 5065 2055 2964 864 2627 2794 842 317 3699 2030 3603 1921 5124 1690 812 1819 1810 786 440 3171 4539 2823 1887 509 5100 2606 688 714 692 349 5880 4436 258 819 5267 5093 4671 4474 2454 2710 2100 1897 3602 5942 2716 3897 1336 5997 4940 3929 5849 2925 2157 1955 5214 2428 3444 3445 3841 5241 3071 2249 2013 5330 1168 1741 5760 5406 5911 4633 259 1608 2783 1763 5218 1135 790 483 4630 4544 3163 1136 2834 3723 1457 5610 2114 1693 3465 5677 851 4132 2972 1139 4583 739 2009 4710 2288 4204 2795 2575 1490 1440 3202 1820 260 4044 1836 1517 469 472 4685 4660 1965 395 3794 850 2334 4383 3952 4470 4581 1356 445 2919 4973 4378 1131 5342 4632 841 2308 5502 4374 3027 2775 5398 5493 4587 2246 4158 5428 5424 5486 3738 2871 3326 1388 1186 4617 4665 2173 1977 3520 5383 740 944 5256 3999 5377 2893 3670 5050 635 2452 5361 1124 404 3850 1729 5353 2467 510 4730 2006 261 1654 2402 2404 2041 5228 3420 763 2695 3413 4603 655 4394 1611 1414 657 2615 3893 816 1527 4641 3162 4477 5712 3618 1080 1146 3802 1822 1816 5065 2055 842 1408 317 5584 3699 5124 1690 1819 1810 509 4205 4092 349 5880 3818 4853 2461 5441 3933 3821 262 1708 3917 500 4609 1947 2663 1047 4297 4121 1377 5581 4788 5495 1672 2519 1432 5702 5869 1215 2346 3226 4964 2277 287 3315 5682 3279 3256 482 4073 354 3034 5033 5814 3705 952 1905 4496 2226 263 1747 1745 3398 2767 3365 4273 3896 3341 3338 4589 3089 5094 5892 356 355 2457 451 1341 1877 4239 1044 5390 3079 1097 4806 3075 810 1422 3844 5246 4083 4187 1143 1140 3656 1519 5245 264 3886 3014 1021 3644 2625 461 729 4941 2332 3595 2486 494 5265 302 1374 1797 3348 3084 4391 975 1910 6022 505 3151 3693 2685 4309 2155 622 1102 2548 368 5858 2993 2803 3777 2852 4526 876 3264 3280 1112 5664 265 5789 1262 5043 4489 3122 4398 382 4030 1938 1714 4552 1055 496 2038 4246 1294 1566 1459 458 1652 2082 2776 4519 2023 2649 2283 5796 4293 5140 4313 4310 3901 4068 3311 4688 1612 4100 1293 820 1996 845 3195 2135 4466 3814 5996 4810 3244 266 4046 4476 5754 1751 959 1475 3927 2035 2665 532 2678 3029 4883 465 5979 5725 2504 2382 4891 1149 1606 1410 3588 3976 4572 3006 3435 1492 5622 1355 2788 1630 709 3934 4252 2220 538 1123 5613 2192 807 3646 4684 1252 4224 5644 5057 4543 605 575 3971 1959 4016 4723 4862 5437 3872 5463 3037 5761 4995 4646 3272 518 4472 1269 5780 1441 5945 1677 4798 4825 5200 849 1892 6019 595 1256 813 734 5753 497 2431 267 1394 3886 6016 3375 1814 3376 3335 3438 504 2865 4535 2048 4349 485 971 3571 3677 3253 478 4443 4437 5075 4715 3287 6010 4629 2096 1635 2892 3023 5125 3567 3570 3574 1657 5172 3959 295 4714 4712 4709 787 4227 854 3137 3130 5866 1991 493 5084 5676 2363 5808 872 3004 5787 5807 835 4969 4967 3284 1401 2495 4203 3131 5156 1545 5176 4212 2376 4882 2973 2161 1597 6006 5106 2416 4226 4533 555 1639 4170 3339 5145 3345 927 1451 2993 5181 3303 3343 2128 3217 894 268 5343 2766 4329 1869 3051 2897 1225 1224 2836 2833 2867 2813 2832 2728 2883 2693 2090 2811 1603 1634 808 1300 1930 1927 2692 2732 2681 1831 4465 2072 4062 4438 4413 4410 4409 1324 1319 1962 5215 2108 1688 915 5799 3040 3314 5404 3294 5367 5436 1345 3208 3292 3310 3982 3317 2448 5293 670 1273 3498 2930 1472 1501 4345 1468 3481 1499 5698 2397 2047 2660 2659 1853 5167 5168 5296 5295 4739 2831 4600 776 778 825 3768 4295 4733 4291 822 3769 3701 1738 702 1748 4951 4597 2034 3880 3899 5988 3240 2709 5280 2068 4471 725 723 4364 4861 4829 4823 4824 1218 4727 3984 1203 1287 3924 755 3918 5733 3637 2298 1318 1916 930 2297 519 1883 1885 1884 5822 587 4564 3913 4595 2591 3708 2253 5841 677 710 3915 4728 4732 5825 4735 2037 2012 4725 5071 1711 4590 3590 5842 384 5368 4486 325 4072 5853 1033 1692 2610 976 1465 1554 1496 1904 1899 3907 768 837 838 970 1670 3767 269 4242 4060 4063 4012 4015 4002 4057 439 5425 1604 3233 2419 5784 270 3014 2332 1438 2590 3405 2127 5639 2310 5262 3871 302 1374 1797 5839 1503 2395 2471 4175 3647 3900 4986 5115 4323 3909 2886 4037 2289 2274 3586 5930 5281 533 361 357 1026 2473 1767 2113 279 5630 5936 1989 5117 3838 3124 3151 359 449 2343 4907 2316 5555 5554 5552 5573 1625 5550 5548 5529 2896 5261 4778 3664 4478 5109 733 4906 2479 3772 772 3626 607 5655 4605 4592 1540 4130 941 3529 4004 622 2539 2993 876 315 271 2850 4029 5797 5717 1761 434 1922 5077 4565 5577 4359 5151 4819 1967 4653 3015 1439 4537 3238 678 4272 5223 5671 5844 4090 1007 5624 3157 5003 2853 1005 4053 428 3216 978 2534 5372 966 3415 2768 935 5179 3749 3198 1206 4918 4468 1736 2543 3797 1641 4571 4663 446 5511 4196 310 5481 748 329 4827 524 272 1948 2237 3052 2561 4697 5960 2487 5068 3207 4549 1018 2430 4584 4461 5598 3276 5166 1072 5111 5127 5697 747 1369 634 4898 1558 2922 2240 477 1811 1091 4435 3559 2265 1050 943 3211 1048 2392 2383 2971 3333 2207 2619 3883 4306 2802 3981 5896 5188 5792 5180 4274 4270 5583 814 3948 4275 1523 5700 588 940 1906 5530 1889 1973 5272 4047 4147 3022 5042 3177 4499 1866 5898 3911 5707 4346 3184 968 5752 2258 5627 1498 358 3492 419 3762 1171 5433 5621 3760 1681 3367 991 273 1163 2076 1830 1303 4069 544 562 4165 4167 4174 2963 1304 5852 5848 5854 4109 4448 3733 3579 3584 828 4429 4430 5631 1784 4483 2330 3073 1205 481 2301 2915 5859 3148 1460 4538 4580 3127 3938 4770 1354 1382 281 283 5921 1161 1160 5603 1162 601 4104 4105 3811 4649 4651 4106 1544 5916 933 599 473 1637 3112 3621 2312 3039 1915 5487 5066 5776 2737 612 1366 904 794 5868 3606 5565 274 3538 5649 2228 2704 3658 459 3828 727 5028 2087 275 3886 4043 3014 3644 2625 4941 1021 461 729 1438 2590 3405 4525 360 3595 2486 2310 302 1797 5169 5483 2289 2274 3348 1901 3344 3084 3586 4269 3926 2604 762 5591 342 3722 2473 975 1999 3151 3282 3848 2819 4984 3302 3219 1867 1102 368 3777 2852 2863 876 3264 276 1043 1753 5074 408 2632 2112 4101 5032 5640 2502 3007 3380 4968 1009 5983 5963 4522 2551 557 2043 4579 4365 5224 3960 1372 5863 2864 1891 3597 5259 5234 6001 3319 5239 2822 2670 4341 3920 2352 2354 4445 2478 2934 742 1516 827 1671 1117 1842 5291 5883 3458 5711 5659 2931 4013 277 4766 1313 3531 980 2159 2935 906 4416 1068 3895 2559 278 4983 639 5014 5431 2860 3082 3324 1578 4195 2196 4856 2717 3229 3455 2726 3726 376 4514 528 1337 362 3744 363 1081 2913 877 1764 3360 1803 3525 856 1310 1237 1233 744

Example 3 Consensus Sequence Build

ClustalW program is selected for multiple sequence alignments of an amino acid sequence of SEQ ID NO: 140 and its homologs, through SEQ ID NO: 278 and its homologs. Three major factors affecting the sequence alignments dramatically are (1) protein weight matrices; (2) gap open penalty; (3) gap extension penalty. Protein weight matrices available for ClustalW program include Blosum, Pam and Gonnet series. Those parameters with gap open penalty and gap extension penalty were extensively tested. On the basis of the test results, Blosum weight matrix, gap open penalty of 10 and gap extension penalty of 1 were chosen for multiple sequence alignment. The consensus sequence of SEQ ID NO: 237 and its 9 homologs were derived according to the procedure described above and is displayed in FIGS. 4(a) and 4(b). FIG. 4(b) is a continuation of FIG. 4(a). SEQ ID NO: 6033 is the consensus sequence built.

Example 4 Pfam Module Annoation

This example illustrates the identification of domain and domain module by Pfam analysis.

The amino acid sequence of the expressed proteins that were shown to be associated with an enhanced trait were analyzed for Pfam protein family against the current Pfam collection of multiple sequence alignments and hidden Markov models using the HMMER software in the appended computer listing. The Pfam domain modules and individual protein domain for the proteins of SEQ ID NO: 140 through 278 are shown in Table 17 and Table 18 respectively. The Hidden Markov model databases for the identified patent families are also in the appended computer listing allowing identification of other homologous proteins and their corresponding DNA to enable the full breadth of the invention for a person of ordinary skill in the art. Certain proteins are identified by a single Pfam domain and others by multiple Pfam domains. For instance, the protein with amino acids of SEQ ID NO: 180 is characterized by two Pfam domains, e.g. “Homeobox” and “HALZ”. See also the protein with amino acids of SEQ ID NO: 248 which is characterized by two copies of the Pfam domain “Ank”. In Table 18 “score” is the gathering score for the Hidden Markov Model of the domain which exceeds the gathering cutoff reported in Table 19.

TABLE 17 PEP Seq ID No. Construct ID Pfam module Position 217 CGPG3875.pep WRKY::WRKY 204-262::343-402 169 CGPG2811.pep AP2 206-257 252 CGPG7367.pep AUX_IAA  66-359 207 CGPG3825.pep WRKY 102-164 213 CGPG3858.pep WRKY 146-205 192 CGPG3451.pep HLH 43-95 176 CGPG2985.pcp Myb_DNA-binding::Linker_histone 5-57::123-189 259 CGPG7655.pcp zf-B_box::zf-B_box 1-47::53-100 181 CGPG3287.pep Ank::Ank::Auk::Chromo 127-158::159- 191::193-225::320-368 236 CGPG4612.pep NAM  6-141 185 CGPG3309.pep zf-C2H2 68-90 171 CGPG2935.pep Myb_DNA-binding 30-75 186 CGPG3312.pep bZIP 1 146-209 250 CGPG690.pep PHD 196-246 245 CGPG5324.pep Linker_histone::AT_hook::AT_hook::AT_hook::AT_hook 11-78::84-96::106- 118::132-144::156-168 159 CGPG2699.pep B3::Auxin_resp 176-281::302-384 150 CGPG2594.pep HLH 277-327 253 CGPG7369.pep zf-Dof  38-100 258 CGPG7641.pep AT_hook::DUF296 70-82::142-262 239 CGPG5130.pep AT_hook::AT_hook::DUF296 105-117::147- 159::177-296 164 CGPG2757.pep NAM  3-139 182 CGPG3289.pep GATA 43-78 205 CGPG3813.pep NAM  16-145 218 CGPG3879.pep Myb_DNA-binding 235-286 269 CGPG7840.pep zf-B_box::CCT 1-47::367-411 232 CGPG4525.pep POX::Homeobox 261-385::426-484 265 CGPG7748.pep B3::Auxin_resp::AUX_IAA 141-246::268- 350::640-805 220 CGPG3987.pep Myb_DNA-binding::Myb_DNA-binding 13-59::65-110 255 CGPG7374.pep Myb_DNA-binding::Myb_DNA-binding 38-84::90-135 214 CGPG3865.pep zf-C2H2 67-89 201 CGPG3793.pep zf-C2H2 243-265 152 CGPG2604.pep Myb_DNA-binding::Myb_DNA-binding 30-79::126-173 178 CGPG3169.pep Myb_DNA-binding::Myb_DNA-binding 18-65::71-116 233 CGPG4527.pep TCP  96-305 175 CGPG2975.pep KNOX1::KNOX2 83-127::134-185 166 CGPG2778.pep zf-ZPR1::zf-ZPR1 32-193::283-444 260 CGPG7678.pep Myb_DNA-binding::Myb_DNA-binding 8-55::61-106 276 CGPG6312.pep DUF630::DUF632 1-60::186-502 256 CGPG7376.pep WRKY  84-144 242 CGPG5292.pep Myb_DNA-binding  88-135 145 CGPG2551.pep zf-C2H2 60-82 202 CGPG3795.pep HLH 230-280 174 CGPG2961.pep AP2 129-180 154 CGPG2639.pep AT_hook::DUF296 80-92::107-232 248 CGPG5422.pep Ank::Ank::Ank::Ank::Ank 36-68::70-102:104- 137::138-170::184-226 183 CGPG3296.pep WRKY 216-276 167 CGPG2797.pep zf-C2H2 206-228 261 CGPG7697.pep NAM  14-140 195 CGPG3476.pep AP2 41-92 257 CGPG7378.pep NAM  25-156 244 CGPG5316.pep Myb_DNA-binding::Myb_DNA- 60-106::112- binding::Myb_DNA-binding 158::164-209 216 CGPG3869.pep NAM  6-134 148 CGPG2586.pep HLH 154-204 168 CGPG2805.pep Myb_DNA-binding::Myb_DNA-binding 20-67::73-118 177 CGPG3107.pep Myb_DNA-binding 243-294 274 CGPG4213.pep HLH  63-112 225 CGPG4066.pep bZIP_2  69-119 184 CGPG3298.pep bZIP_2 192-246 241 CGPG5280.pep BAH::PHD 21-136::140-189 155 CGPG2644.pep HLH 132-181 199 CGPG3750.pep NAM  7-136 163 CGPG2752.pep GATA 222-257 266 CGPG7757.pep SSrecog::Rtt106::HMG_box 219-434::359- 500::556-624 141 CGPG1754.pep DUF573 153-246 206 CGPG382.pep zf-B_box::CCT 11-59::357-401 210 CGPG3841.pep HLH 211-260 142 CGPG1809.pep RWP-RK 144-195 238 CGPG490.pep AP2::B3 81-130::209-330 144 CGPG2164.pep AUX_IAA 266-436 173 CGPG2948.pep SRF-TF 20-73 264 CGPG7743.pep AP2 164-215 212 CGPG3857.pep AP2  74-125 221 CGPG4004.pep HSF_DNA-bind  42-212 267 CGPG7759.pep AP2 27-78 151 CGPG26.pep SRF-TF::K-box 9-59::75-174 196 CGPG3505.pep Myb_DNA-binding 47-98 262 CGPG7709.pep zf-LSD1::zf-LSD1::zf-LSD1 7-31::46-70::82-106 231 CGPG4195.pep KNOX1::KNOX2::ELK 18-62::73-128::184-205 228 CGPG4112.pep zf-C3HC4 202-242 204 CGPG3810.pep MFMR::bZIP_1 1-205::293-356 277 CGPG7188.pep DUF573 120-211 211 CGPG3843.pep Myb_DNA-binding  84-135 149 CGPG2593.pep HLH 163-214 153 CGPG2615.pep NAM  9-138 198 CGPG367.pep Myb_DNA-binding::Myb_DNA-binding 14-61::67-112 243 CGPG5306.pep SRF-TF::K-box 9-59::76-173 187 CGPG3327.pep zf-C3HC4 109-149 235 CGPG4591.pep zf-B_box  1-46 251 CGPG7354.pep WRKY 159-219 194 CGPG3468.pep zf-B_box::CCT 10-57::265-309 273 CGPG31.pep EIN3  31-422 272 CGPG2562.pep HSF_DNA-bind  18-188 263 CGPG7714.pep AUX_IAA  6-173 208 CGPG3828.pep TCP  44-253 146 CGPG2578.pep Myb_DNA-binding::Myb_DNA-binding 25-72::78-123 275 CGPG477.pep AP2 37-88 268 CGPG7822.pep KNOX1::KNOX2::ELK::Homeobox 32-76::79-130::178- 199::201-260 254 CGPG7373.pep HSF_DNA-bind  14-194 229 CGPG4133.pep HSF_DNA-bind  8-206 224 CGPG4061.pep AP2::B3 75-124::204-318 230 CGPG4166.pep NAM  11-139 161 CGPG2711.pep SBP  58-136 246 CGPG5330.pep AP2 128-180 179 CGPG3171.pep zf-C2H2 61-83 147 CGPG2583.pep SRF-TF::K-box 9-59::79-173 170 CGPG2907.pep zf-C2H2 177-200 200 CGPG3761.pep GRAS  1-320 222 CGPG4013.pep AP2 119-170 172 CGPG2943.pep Myb_DNA-binding  65-110 270 CGPG7876.pep AP2 21-72 140 CGPG113.pep AP2-AP2 282-342::384-436 226 CGPG4082.pep HLH 127-178 271 CGPG858.pep CXC::CXC 398-439::484-525 156 CGPG2657.pep AP2 25-76 215 CGPG3868.pep NAM  17-139 197 CGPG359.pep zf-C3HC4  89-132 223 CGPG4015.pep Myb_DNA-binding::Myb_DNA-binding 14-61::67-112 190 CGPG3369.pep GRAS 130-436 180 CGPG3175.pep Homeobox::HALZ 30-86::87-131 247 CGPG5334.pep Myb_DNA-binding 109-156 227 CGPG4106.pep NAM  9-134 203 CGPG3804.pep WRKY 135-194 209 CGPG3837.pep zf-C2H2 244-266 193 CGPG3463.pep zf-C2H2  6-28 240 CGPG5278.pep NAM  20-146 165 CGPG2767.pep zf-C2H2 193-215 188 CGPG3341.pep AP2::AP2 130-180::222-273 158 CGPG2678.pep zf-C3HC4 113-153 249 CGPG5599.pep RWP-RK::PB1 605-656::811-894 219 CGPG3947.pep SRF-TF::K-box 9-59::75-174 157 CGPG2664.pep zf-B_box 26-72

TABLE 18 PEP Pfam Seq ID No. Construct ID domain name Begin Stop score E-value 140 CGPG113.pep AP2 282 342 60.7 4.90E−15 140 CGPG113.pep AP2 384 436 64.2 4.50E−16 141 CGPG1754.pep DUF573 153 246 225.4 1.30E−64 142 CGPG1809.pep RWP-RK 144 195 76 1.20E−19 144 CGPG2164.pep AUX_IAA 266 436 −74.9 0.00043 145 CGPG2551.pep zf-C2H2 60 82 24.2 0.00048 146 CGPG2578.pep Myb_DNA-binding 25 72 47.2 5.90E−11 146 CGPG2578.pep Myb_DNA-binding 78 123 46.4 9.80E−11 147 CGPG2583.pep SRF-TF 9 59 107.5 4.10E−29 147 CGPG2583.pep K-box 79 173 44.6 3.50E−10 148 CGPG2586.pep HLH 154 204 27.2 5.90E−05 149 CGPG2593.pep HLH 163 214 43.8 6.00E−10 150 CGPG2594.pep HLH 277 327 66.3 1.00E−16 151 CGPG26.pep SRF-TF 9 59 119.5 1.00E−32 151 CGPG26.pep K-box 75 174 166.3 8.30E−47 152 CGPG2604.pep Myb_DNA-binding 30 79 31 4.30E−06 152 CGPG2604.pep Myb_DNA-binding 126 173 45 2.70E−10 153 CGPG2615.pep NAM 9 138 293.9 3.10E−85 154 CGPG2639.pep AT_hook 80 92 7.5 1.2 154 CGPG2639.pep DUF296 107 232 209.5 8.00E−60 155 CGPG2644.pep HLH 132 181 51 4.10E−12 156 CGPG2657.pep AP2 25 76 78.3 2.60E−20 157 CGPG2664.pep zf-B_box 26 72 43.1 1.00E−09 158 CGPG2678.pep zf-C3HC4 113 153 44.5 3.70E−10 159 CGPG2699.pep B3 176 281 104.7 2.80E−28 159 CGPG2699.pep Auxin_resp 302 384 204.5 2.50E−58 161 CGPG2711.pep SBP 58 136 173.4 6.00E−49 163 CGPG2752.pep GATA 222 257 75.4 1.90E−19 164 CGPG2757.pep NAM 3 139 145.1 2.00E−40 165 CGPG2767.pep zf-C2H2 193 215 21.8 0.0025 166 CGPG2778.pep zf-ZPR1 32 193 253 6.50E−73 166 CGPG2778.pep zf-ZPR1 283 444 207.6 3.00E−59 167 CGPG2797.pep zf-C2H2 206 228 30.5 6.00E−06 168 CGPG2805.pep Myb_DNA-binding 20 67 42.7 1.30E−09 168 CGPG2805.pep Myb_DNA-binding 73 118 50.8 4.80E−12 169 CGPG2811.pep AP2 206 257 32.1 2.00E−06 170 CGPG2907.pep zf-C2H2 177 200 24.1 0.00052 171 CGPG2935.pep Myb_DNA-binding 30 75 32.3 1.80E−06 172 CGPG2943.pep Myb_DNA-binding 65 110 57.6 4.40E−14 173 CGPG2948.pep SRF-TF 20 73 27.1 6.40E−05 174 CGPG2961.pep AP2 129 180 65 2.50E−16 175 CGPG2975.pep KNOX1 83 127 94.4 3.50E−25 175 CGPG2975.pep KNOX2 134 185 114.1 4.10E−31 176 CGPG2985.pep Myb_DNA-binding 5 57 34.7 3.30E−07 176 CGPG2985.pep Linker_histone 123 189 0.3 0.00099 177 CGPG3107.pep Myb_DNA-binding 243 294 44.6 3.60E−10 178 CGPG3169.pep Myb_DNA-binding 18 65 53.4 7.80E−13 178 CGPG3169.pep Myb_DNA-binding 71 116 59 1.60E−14 179 CGPG3171.pep zf-C2H2 61 83 21.8 0.0026 180 CGPG3175.pep Homeobox 30 86 66.5 8.90E−17 180 CGPG3175.pep HALZ 87 131 37.6 4.30E−08 181 CGPG3287.pep Ank 127 158 6.6 3.7 181 CGPG3287.pep Ank 159 191 24.8 0.00033 181 CGPG3287.pep Ank 193 225 30.7 5.50E−06 181 CGPG3287.pep Chromo 320 368 45.7 1.60E−10 182 CGPG3289.pep GATA 43 78 65.8 1.50E−16 183 CGPG3296.pep WRKY 216 276 141 3.30E−39 184 CGPG3298.pep bZIP_2 192 246 31 4.30E−06 184 CGPG3298.pep bZIP_1 194 255 26.8 8.00E−05 185 CGPG3309.pep zf-C2H2 68 90 20.4 0.0066 186 CGPG3312.pep bZIP_1 146 209 34.3 4.50E−07 186 CGPG3312.pep bZIP_2 146 200 28.6 2.40E−05 187 CGPG3327.pep zf-C3HC4 109 149 49 1.60E−11 188 CGPG3341.pep AP2 130 180 62.3 1.60E−15 188 CGPG3341.pep AP2 222 273 58.2 2.90E−14 190 CGPG3369.pep GRAS 130 436 532.9  3.50E−157 192 CGPG3451.pep HLH 43 95 33.5 7.80E−07 193 CGPG3463.pep zf-C2H2 6 28 24.2 0.00047 194 CGPG3468.pep zf-B_box 10 57 39.9 9.30E−09 194 CGPG3468.pep CCT 265 309 86.2 1.00E−22 195 CGPG3476.pep AP2 41 92 73.1 9.10E−19 196 CGPG3505.pep Myb_DNA-binding 47 98 43.1 1.00E−09 197 CGPG359.pep zf-C3HC4 89 132 35.3 2.30E−07 198 CGPG367.pep Myb_DNA-binding 14 61 46.6 8.70E−11 198 CGPG367.pep Myb_DNA-binding 67 112 53.8 6.00E−13 199 CGPG3750.pep NAM 7 136 307.5 2.50E−89 200 CGPG3761.pep GRAS 1 320 391.8  1.00E−114 201 CGPG3793.pep zf-C2H2 243 265 22.2 0.002 202 CGPG3795.pep HLH 230 280 33.3 8.80E−07 203 CGPG3804.pep WRKY 135 194 153.9 4.40E−43 204 CGPG3810.pep MFMR 1 205 368.8  9.00E−108 204 CGPG3810.pep bZIP_1 293 356 91.5 2.60E−24 204 CGPG3810.pep bZIP_2 293 347 29.2 1.50E−05 205 CGPG3813.pep NAM 16 145 295.2 1.20E−85 206 CGPG382.pep zf-B_box 11 59 38 3.40E−08 206 CGPG382.pep CCT 357 401 85.6 1.60E−22 207 CGPG3825.pep WRKY 102 164 94.6 3.10E−25 208 CGPG3828.pep TCP 44 253 149.4 1.00E−41 209 CGPG3837.pep zf-C2H2 244 266 24.8 0.00032 210 CGPG3841.pep HLH 211 260 44.6 3.50E−10 211 CGPG3843.pep Myb_DNA-binding 84 135 47.7 4.00E−11 212 CGPG3857.pep AP2 74 125 83.2 8.60E−22 213 CGPG3858.pep WRKY 146 205 144.2 3.80E−40 214 CGPG3865.pep zf-C2H2 67 89 22.1 0.0021 215 CGPG3868.pep NAM 17 139 58.4 2.50E−14 216 CGPG3869.pep NAM 6 134 304.9 1.50E−88 217 CGPG3875.pep WRKY 204 262 141.3 2.70E−39 217 CGPG3875.pep WRKY 343 402 151.5 2.30E−42 218 CGPG3879.pep Myb_DNA-binding 235 286 35.8 1.60E−07 219 CGPG3947.pep SRF-TF 9 59 118.6 1.90E−32 219 CGPG3947.pep K-box 75 174 165.8 1.20E−46 220 CGPG3987.pep Myb_DNA-binding 13 59 59.2 1.40E−14 220 CGPG3987.pep Myb_DNA-binding 65 110 50.8 4.90E−12 221 CGPG4004.pep HSF_DNA-bind 42 212 267.1 3.60E−77 222 CGPG4013.pep AP2 119 170 87.4 4.70E−23 223 CGPG4015.pep Myb_DNA-binding 14 61 46.6 8.80E−11 223 CGPG4015.pep Myb_DNA-binding 67 112 40.9 4.40E−09 224 CGPG4061.pep AP2 75 124 50.7 5.30E−12 224 CGPG4061.pep B3 204 318 116.1 1.00E−31 225 CGPG4066.pep bZIP_2 69 119 24.4 0.00043 226 CGPG4082.pep HLH 127 178 59.2 1.40E−14 227 CGPG4106.pep NAM 9 134 300.7 2.80E−87 228 CGPG4112.pep zf-C3HC4 202 242 39.7 1.00E−08 229 CGPG4133.pep HSF_DNA-bind 8 206 179.6 7.80E−51 230 CGPG4166.pep NAM 11 139 316.4 5.10E−92 231 CGPG4195.pep KNOX1 18 62 72.1 1.90E−18 231 CGPG4195.pep KNOX2 73 128 86.8 7.00E−23 231 CGPG4195.pep ELK 184 205 25.4 0.0002 232 CGPG4525.pep POX 261 385 200.7 3.60E−57 232 CGPG4525.pep Homeobox 426 484 6.6 0.0024 233 CGPG4527.pcp TCP 96 305 303.9 3.10E−88 235 CGPG4591.pep zf-B_box 1 46 22.6 0.00055 236 CGPG4612.pep NAM 6 141 278.3 1.60E−80 238 CGPG490.pep AP2 81 130 55.4 1.90E−13 238 CGPG490.pep B3 209 330 110.8 4.00E−30 239 CGPG5130.pep AT_hook 105 117 19 0.013 239 CGPG5130.pep AT_hook 147 159 6.3 1.9 239 CGPG5130.pep DUF296 177 296 206.6 6.00E−59 240 CGPG5278.pep NAM 20 146 307.2 3.00E−89 241 CGPG5280.pep BAH 21 136 139.8 7.60E−39 241 CGPG5280.pep PHD 140 189 56.9 6.90E−14 242 CGPG5292.pep Myb_DNA-binding 88 135 49 1.70E−11 243 CGPG5306.pep SRF-TF 9 59 98.7 1.90E−26 243 CGPG5306.pep K-box 76 173 133.1 8.00E−37 244 CGPG5316.pep Myb_DNA-binding 60 106 51.8 2.40E−12 244 CGPG5316.pep Myb_DNA-binding 112 158 59.9 8.70E−15 244 CGPG5316.pep Myb_DNA-binding 164 209 45.4 2.00E−10 245 CGPG5324.pep Linker_histone 11 78 93.2 8.30E−25 245 CGPG5324.pep AT_hook 84 96 9.3 0.6 245 CGPG5324.pep AT_hook 106 118 16.7 0.031 245 CGPG5324.pep AT_hook 132 144 11.7 0.23 245 CGPG5324.pep AT_hook 156 168 13.4 0.12 246 CGPG5330.pep AP2 128 180 85.5 1.70E−22 247 CGPG5334.pep Myb_DNA-binding 109 156 48.1 3.10E−11 248 CGPG5422.pep Ank 36 68 3.5 10 248 CGPG5422.pep Ank 70 102 9.1 1.6 248 CGPG5422.pep Ank 104 137 11 0.85 248 CGPG5422.pep Ank 138 170 8.5 2 248 CGPG5422.pep Ank 184 226 13.3 0.39 249 CGPG5599.pep RWP-RK 605 656 106.1 1.10E−28 249 CGPG5599.pep PB1 811 894 87.3 5.00E−23 250 CGPG690.pep PHD 196 246 53.8 5.80E−13 251 CGPG7354.pep WRKY 159 219 139.2 1.20E−38 252 CGPG7367.pep AUX_IAA 66 359 448.6  8.70E−132 253 CGPG7369.pep zf-Dof 38 100 138.6 1.80E−38 254 CGPG7373.pep HSF_DNA-bind 14 194 189.2 1.00E−53 255 CGPG7374.pep Myb_DNA-binding 38 84 57.8 3.80E−14 255 CGPG7374.pep Myb_DNA-binding 90 135 58.8 1.80E−34 256 CGPG7376.pep WRKY 84 144 130.5 4.70E−36 257 CGPG7378.pep NAM 25 156 247.7 2.50E−71 258 CGPG7641.pep AT_hook 70 82 19.1 0.012 258 CGPG7641.pep DUF296 142 262 232.7 8.20E−67 259 CGPG7655.pep zf-B_box 1 47 41.2 3.60E−09 259 CGPG7655.pep zf-B_box 53 100 54.5 3.80E−13 260 CGPG7678.pep Myb_DNA-binding 8 55 50.2 7.30E−12 260 CGPG7678.pep Myb_DNA-binding 61 106 57.2 5.50E−14 261 CGPG7697.pep NAM 14 140 299.2 7.80E−87 262 CGPG7709.pep zf-LSD1 7 31 38.1 3.20E−08 262 CGPG7709.pep zf-LSD1 46 70 52 2.10E−12 262 CGPG7709.pep zf-LSD1 82 106 46.7 8.20E−11 263 CGPG7714.pep AUX_IAA 6 173 339.7 5.10E−99 264 CGPG7743.pep AP2 164 215 80.1 7.30E−21 265 CGPG7748.pep B3 141 246 110.7 4.50E−30 265 CGPG7748.pep Auxin_resp 268 350 198.6 1.50E−56 265 CGPG7748.pep AUX_IAA 640 805 −72.2 0.00028 266 CGPG7757.pep SSrecog 219 434 495.1  8.70E−146 266 CGPG7757.pep Rtt106 359 500 179.1 1.20E−50 266 CGPG7757.pep HMG_box 556 624 110.2 6.50E−30 267 CGPG7759.pep AP2 27 78 79.5 1.10E−20 268 CGPG7822.pep KNOX1 32 76 81.2 3.30E−21 268 CGPG7822.pep KNOX2 79 130 92.5 1.30E−24 268 CGPG7822.pep ELK 178 199 30 8.50E−06 268 CGPG7822.pep Homeobox 201 260 0.4 0.0098 269 CGPG7840.pep zf-B_box 1 47 23.5 0.00044 269 CGPG7840.pep CCT 367 411 80.2 6.50E−21 270 CGPG7876.pep AP2 21 72 82.5 1.40E−21 271 CGPG858.pep CXC 398 439 89.7 9.20E−24 271 CGPG858.pep CXC 484 525 82.7 1.10E−21 272 CGPG2562.pep HSF_DNA-bind 18 188 213.9 3.70E−61 273 CGPG31.pep EIN3 31 422 1032.5 0 274 CGPG4213.pep HLH 63 112 44.3 4.40E−10 275 CGPG477.pep AP2 37 88 79.6 9.90E−21 276 CGPG6312.pep DUF630 1 60 123.9 4.80E−34 276 CGPG6312.pep DUF632 186 502 465.8  5.80E−137 277 CGPG7188.pep DUF573 120 211 191.2 2.60E−54

TABLE 19 Pfam gathering domain name Accession # cutoff domain description AT_hook PF02178.10 3.6 AT hook motif AUX_IAA PF02309.7 −83 AUX/IAA family Ank PF00023.21 0 Ankyrin repeat Auxin_resp PF06507.4 25 Auxin response factor B3 PF02362.12 26.5 B3 DNA binding domain BAH PF01426.9 7 BAH domain CCT PF06203.5 25 CCT motif CXC PF03638.6 25 Tesmin/TSO1-like CXC domain Chromo PF00385.15 27.5 ‘chromo’ (CHRromatin Organisation MOdifier) domain DUF296 PF03479.6 −11 Domain of unknown function (DUF296) DUF573 PF04504.5 25 Protein of unknown function, DUF573 DUF630 PF04783.3 25 Protein of unknown function (DUF630) DUF632 PF04782.3 25 Protein of unknown function (DUF632) EIN3 PF04873.4 −137.6 Ethylene insensitive 3 ELK PF03789.4 25 ELK domain GATA PF00320.18 28.5 GATA zinc finger GRAS PF03514.5 −78 GRAS family transcription factor HALZ PF02183.9 18.1 Homeobox associated leucine zipper HLH PF00010.17 8.3 Helix-loop-helix DNA-binding domain HMG_box PF00505.10 4.1 HMG (high mobility group) box HSF_DNA-bind PF00447.8 −70 HSF-type DNA-binding Homeobox PF00046.20 −4.1 Homeobox domain K-box PF01486.8 0 K-box region KNOX1 PF03790.4 25 KNOX1 domain KNOX2 PF03791.4 25 KNOX2 domain Linker_histone PF00538.10 −8 linker histone H1 and H5 family MFMR PF07777.2 −46.7 G-box binding protein MFMR Myb_DNA- PF00249.22 14 Myb-like DNA-binding domain binding NAM PF02365.6 −19 No apical meristem (NAM) protein PB1 PF00564.15 12.3 PB1 domain PHD PF00628.20 26.2 PHD-finger POX PF07526.2 −39.4 Associated with HOX RWP-RK PF02042.6 25 RWP-RK domain Rtt106 PF08512.3 10.1 Histone chaperone Rttp106-like SBP PF03110.5 25 SBP domain SRF-TF PF00319.9 11 SRF-type transcription factor (DNA-binding and dimerisation domain) SSrecog PF03531.5 −73.6 Structure-specific recognition protein (SSRP1) TCP PF03634.4 −38 TCP family transcription factor WRKY PF03106.6 −6.7 WRKY DNA -binding domain bZIP_1 PF00170.12 24.8 bZIP transcription factor bZIP_2 PF07716.6 15 Basic region leucine zipper zf-B_box PF00643.15 15.3 B-box zinc finger zf-C2H2 PF00096.17 17.7 Zinc finger, C2H2 type zf-C3HC4 PF00097.16 16 Zinc finger, C3HC4 type (RING finger) zf-Dof PF02701.6 25 Dof domain, zinc finger zf-LSD1 PF06943.3 25 LSD1 zinc finger zf-ZPR1 PF03367.4 25 ZPR1 zinc-finger domain

Example 5 Plasmid Construction for Transferring Recombinant DNA

This example illustrates the construction of plasmids for transferring recombinant DNA into the nucleus of a plant cell which can be regenerated into a transgenic crop plant of this invention. Primers for PCR amplification of protein coding nucleotides of recombinant DNA are designed at or near the start and stop codons of the coding sequence, in order to eliminate most of the 5′ and 3′ untranslated regions. DNA of interest, e.g., each DNA identified in Table 2 and the DNA for the identified homologous genes, are cloned and amplified by PCR prior to insertion into the insertion site the base vector.

A. Plant Expression Constructs for Corn Transformation

Elements of an exemplary common expression vector, pMON93039 are illustrated in Table 20. The exemplary base vector which is especially useful for corn transformation is illustrated in FIG. 2 and assembled using technology known in the art.

TABLE 20 pMON93039 Coordinates of function name annotation SEQ ID NO: 6024 Agrobacterium B-AGRtu.right border Agro right border 11364-11720 T-DNA sequence, essential for trabsfer transfer of T-DNA. Gene of E-Os.Act1 upstream promoter region  19-775 interest of the rice actin 1 gene expression E-CaMV.35S.2xA1-B3 duplicated35S A1-B3  788-1120 cassette domain without TATA box P-Os.Act1 promoter region of the rice 1125-1204 actin 1 gene L-Ta.Lhcb1 5′ untranslated leader of 1210-1270 wheat major chlorophyll a/b binding protein I-Os.Act1 first intron and flanking 1287-1766 UTR exon sequences from the rice actin 1 gene T-St.Pis4 3′ non-translated region of 1838-2780 the potato proteinase inhibitor II gene which functions to direct polyadenylation of the mRNA Plant P-Os.Act1 Promoter from the rice 2830-3670 selectable actin 1 gene marker L-Os.Act1 first exon of the rice actin 3671-3750 expression 1 gene cassette I-Os.Act1 first intron and flanking 3751-4228 UTR exon sequences from the rice actin 1 gene TS-At.ShkG-CTP2 Transit peptide region of 4238-4465 Arabidopsis EPSPS CR-AGRtu.aroA-CP4.nat coding region for bacterial 4466-5833 strain CP4 native arogA gene T-AGRtu.nos A 3′ non-translated region 5849-6101 of the nopaline synthase gene of Agrobacterium tumefaciens Ti plasmid which functions to direct polyadenylation of the mRNA. Agrobacterium B-AGRtu.left border Agro left border sequence, 6168-6609 T-DNA essential for transfer of transfer T-DNA. Maintenance OR-Ec.oriV-RK2 The vegetative origin of 6696-7092 in E. coli replication from plasmid RK2. CR-Ec.rop Coding region for 8601-8792 repressor of primer from the ColE1 plasmid. Expression of this gene product interferes with primer binding at the origin of replication, keeping plasmid copy number low. OR-Ec.ori-ColE1 The minimal origin of 9220-9808 replication from the E. coli plasmid ColE1. P-Ec.aadA-SPC/STR romoter for Tn7 10339-10380 adenylyltransferase (AAD(3″)) CR-Ec.aadA-SPC/STR Coding region for Tn7 10381-11169 adenylyltransferase (AAD(3″)) conferring spectinomycin and streptomycin resistance. T-Ec.aadA-SPC/STR 3′ UTR from the Tn7 11170-11227 adenylyltransferase (AAD(3″)) gene of E. coli.

B. Plant Expression Constructs for Soybean or Canola Transformation

Plasmids for use in transformation of soybean are also prepared. Elements of an exemplary common expression vector plasmid pMON82053 are shown in Table 21 below. This exemplary soybean transformation base vector illustrated in FIG. 2 is assembled using the technology known in the art. DNA of interest, e.g., each DNA identified in Table 2 and the DNA for the identified homologous genes, is cloned and amplified by PCR prior to insertion into the insertion site the base vector at the insertion site between the enhanced 35S CaMV promoter and the termination sequence of cotton E6 gene.

TABLE 21 pMON82053 Coordinates of function name annotation SEQ ID NO: 6025 Agrobacterium B-AGRtu.left Agro left border sequence, essential 6144-6585 T-DNA transfer border for transfer of T-DNA. Plant selectable P-At.Act7 Promoter from the arabidopsis actin 7 marker gene expression L-At.Act7 5′UTR of Arabidopsis Act7 gene cassette I-At.Act7 Intron from the Arabidopsis actin7 gene 6624-7861 TS-At.ShkG-CTP2 Transit peptide region of Arabidopsis 7864-8091 EPSPS CR-AGRtu.aroA- Synthetic CP4 coding region with dicot 8092-9459 CP4.nno_At preferred codon usage. T-AGRtu.nos A 3′ non-translated region of the 9466-9718 nopaline synthase gene of Agrobacterium tumefaciens Ti plasmid which functions to direct polyadenylation of the mRNA. Gene of interest P-CaMV.35S-enh Promoter for 35S RNA from CaMV  1-633 expression containing a duplication of the −90 cassette to −350 region. T-Gb.E6-3b 3′ untranslated region from the fiber  688-1002 protein E6 gene of sea-island cotton; Agrobaterium B-AGRtu.right Agro right border sequence, essential for 1033-1389 T-DNA transfer border transfer of T-DNA. Maintenance in OR-Ec.oriV-RK2 The vegetative origin of replication from 5661-6057 E. coli plasmid RK2. CR-Ec.rop Coding region for repressor of primer 3961-4152 from the ColE1 plasmid. Expression of this gene product interferes with primer binding at the origin of replication, keeping plasmid copy number low. OR-Ec.ori-ColE1 The minimal origin of replication from 2945-3533 the E. coli plasmid ColE1. P-Ec.aadA- romoter for Tn7 adenylyltransferase 2373-2414 SPC/STR (AAD(3″)) CR-Ec.aadA- Coding region for Tn7 1584-2372 SPC/STR adenylyltransferase (AAD(3″)) conferring spectinomycin and streptomycin resistance. T-Ec.aadA- 3′ UTR from the Tn7 1526-1583 SPC/STR adenylyltransferase (AAD(3″)) gene of E. coli.

C. Plant Expression Constructs for Cotton Transformation

Plasmids for use in transformation of cotton are also prepared. Elements of an exemplary common expression vector plasmid pMON99053 are shown in Table 22 below and FIG. 3. Primers for PCR amplification of protein coding nucleotides of recombinant DNA are designed at or near the start and stop codons of the coding sequence, in order to eliminate most of the 5′ and 3′ untranslated regions. Each recombinant DNA coding for a protein identified in Table 2 is amplified by PCR prior to insertion into the insertion site within the gene of interest expression cassette of one of the base.

TABLE 22 pMON99053 Coordinates of function name annotation SEQ ID NO: 6026 Agrobacterium B-AGRtu.right Agro right border sequence,  1-357 T-DNA transfer border essential for transfer of T-DNA. Gene of interest Exp-CaMV.35S- Enhanced version of the 35S  388-1091 expression enh + ph.DnaK RNA promoter from CaMV plus cassette the petunia hsp70 5′ untranslated region T-Ps.RbcS2-E9 The 3′ non-translated region of 1165-1797 the pea RbcS2 gene which functions to direct polyadenylation of the mRNA. Plant selectable Exp-CaMV.35S Promoter and 5′ untranslated 1828-2151 marker expression region of the 35S RNA from cassette CaMV CR-Ec.nptII-Tn5 Neomycin Phosphotransferase II 2185-2979 gene that confers resistance to neomycin and kanamycin T-AGRtu.nos A 3′ non-translated region of the 3011-3263 nopaline synthase gene of Agrobacterium tumefaciens Ti plasmid which functions to direct polyadenylation of the mRNA. Agrobacterium B-AGRtu.left Agro left border sequence, 3309-3750 T-DNA transfer border essential for transfer of T-DNA. Maintenance in OR-Ec.oriV-RK2 The vegetative origin of 3837-4233 E. coli replication from plasmid RK2. CR-Ec.rop Coding region for repressor of 5742-5933 primer from the ColE1 plasmid. Expression of this gene product interferes with primer binding at the origin of replication, keeping plasmid copy number low. OR-Ec.ori-ColE1 The minimal origin of replication 6361-6949 from the E. coli plasmid ColE1. P-Ec.aadA- romoter for Tn7 7480-7521 SPC/STR adenylyltransferase (AAD(3″)) CR-Ec.aadA- Coding region for Tn7 7522-8310 SPC/STR adenylyltransferase (AAD(3″)) conferring spectinomycin and streptomycin resistance. T-Ec.aadA- 3′ UTR from the Tn7 8311-8368 SPC/STR adenylyltransferase (AAD(3″)) gene of E. coli.

Example 6 Corn Plant Transformation

This example illustrates the production and identification of transgenic corn cells in seed of transgenic corn plants having an enhanced agronomic trait, e.g., enhanced nitrogen use efficiency, increased yield, enhanced water use efficiency, enhanced tolerance to cold and/or enhanced seed compositions as compared to control plants. Transgenic corn cells are prepared with recombinant DNA expressing each of the protein encoding DNAs listed in Table 2 by Agrobacterium-mediated transformation using the corn transformation constructs as disclosed in Example 5.

Corn transformation is effected using methods disclosed in U.S. Patent Application Publication 2004/0344075 A1 where corn embryos are inoculated and co-cultured with the Agrobacterium tumefaciens strain ABI and the corn transformation vector. To regenerate transgenic corn plants the transgenic callus resulting from transformation is placed on media to initiate shoot development in plantlets which are transferred to potting soil for initial growth in a growth chamber followed by a mist bench before transplanting to pots where plants are grown to maturity. The plants are self fertilized and seed is harvested for screening as seed, seedlings or progeny R2 plants or hybrids, e.g., for yield trials in the screens indicated above.

Many transgenic events which survive to fertile transgenic plants that produce seeds and progeny plants do not exhibit an enhanced agronomic trait. The transgenic plants and seeds having the transgenic cells of this invention which have recombinant DNA imparting the enhanced agronomic traits are identified by screening for nitrogen use efficiency, yield, water use efficiency, cold tolerance and enhanced seed composition.

Example 7 Soybean Plant Transformation

This example illustrates the production and identification of transgenic soybean cells in seed of transgenic soybean plants having an enhanced agronomic trait, e.g., enhanced nitrogen use efficiency, increased yield, enhanced water use efficiency, enhanced tolerance to cold and/or enhanced seed compositions as compared to control plants. Transgenic soybean cells are prepared with recombinant DNA expressing each of the protein encoding DNAs listed in Table 1 by Agrobacterium-mediated transformation using the soybean transformation constructs disclosed in Example 5. Soybean transformation is effected using methods disclosed in U.S. Pat. No. 6,384,301 where soybean meristem explants are wounded then inoculated and co-cultured with the soybean transformation vector, then transferred to selection media for 6-8 weeks to allow selection and growth of transgenic shoots.

The transformation is repeated for each of the protein encoding DNAs identified in Table 2.

Transgenic shoots producing roots are transferred to the greenhouse and potted in soil. Many transgenic events which survive to fertile transgenic plants that produce seeds and progeny plants do not exhibit an enhanced agronomic trait. The transgenic plants and seeds having the transgenic cells of this invention which have recombinant DNA imparting the enhanced agronomic traits are identified by screening for nitrogen use efficiency, yield, water use efficiency, cold tolerance and enhanced seed composition.

Example 8 Selection of Transgenic Plants with Enhanced Agronomic Trait(s)

This example illustrates identification of nuclei of the invention by screening derived plants and seeds for an enhanced trait identified below.

Many transgenic events which survive to fertile transgenic plants that produce seeds and progeny plants will not exhibit an enhanced agronomic trait. Populations of transgenic seed and plants prepared in Examples 6 and 7 are screened to identify those transgenic events providing transgenic plant cells with a nucleus having recombinant DNA imparting an enhanced trait. Each population is screened for enhanced nitrogen use efficiency, increased yield, enhanced water use efficiency, enhanced tolerance to cold and heat, increased level of oil and protein in seed using assays described below. Plant cell nuclei having recombinant DNA with each of the genes identified in Table 2 and the identified homologs are identified in plants and seeds with at least one of the enhanced traits.

A. Selection for Enhanced Nitrogen Use Efficiency

Transgenic corn plants with nuclei of the invention are planted in fields with three levels of nitrogen (N) fertilizer being applied, i.e. low level (0 pounds per acre N), medium level (80 pounds per acre N) and high level (180 pounds per acre N). Liquid 28% or 32% UAN (Urea, Ammonium Nitrogen) are used as the N source and apply by broadcast boom and incorporate with a field cultivator with rear rolling basket in the same direction as intended crop rows. Although there is no N applied in the low level treatment, the soil should still be disturbed in the same fashion as the treated area. Transgenic plants and control plants can be grouped by genotype and construct with controls arranged randomly within genotype blocks. For improved statistical analysis each type of transgenic plant can be tested by 3 replications and across 4 locations. Nitrogen levels in the fields are analyzed before planting by collecting sample soil cores from 0-24″ and 24 to 48″ soil layer. Soil samples are analyzed for nitrate-nitrogen, phosphorus (P), potassium (K), organic matter and pH to provide baseline values. P, K and micronutrients are applied based upon soil test recommendations.

Transgenic corn plants prepared in Example 6 and which exhibit a 2 to 5% yield increase as compared to control plants when grown in the high nitrogen field are selected as having nuclei of the invention. Transgenic corn plants which have at least the same or higher yield as compared to control plants when grown in the medium nitrogen field are selected as having nuclei of the invention. Transgenic corn plants having a nucleus with DNA identified in Table 3 as imparting nitrogen use efficiency (LN) and homologous DNA are selected from a nitrogen use efficiency screen as having a nucleus of this invention.

B. Selection for Increased Yield

Many transgenic plants of this invention exhibit increased yield as compared to a control plant. Increased yield can result from enhanced seed sink potential, e.g., the number and size of endosperm cells or kernels and/or enhanced sink strength, e.g., the rate of starch biosynthesis. Sink potential can be established very early during kernel development, as endosperm cell number and size are determined within the first few days after pollination.

Much of the increase in corn yield of the past several decades has resulted from an increase in planting density. During that period, corn yield has been increasing at a rate of 2.1 bushels/acre/year, but the planting density has increased at a rate of 250 plants/acre/year. A characteristic of modern hybrid corn is the ability of these varieties to be planted at high density. Many studies have shown that a higher than current planting density should result in more biomass production, but current germplasm does not perform well at these higher densities. One approach to increasing yield is to increase harvest index (HI), the proportion of biomass that is allocated to the kernel compared to total biomass, in high density plantings.

Effective yield selection of enhanced yielding transgenic corn events uses hybrid progeny of the transgenic event over multiple locations with plants grown under optimal production management practices, and maximum pest control. A useful target for increased yield is a 5% to 10% increase in yield as compared to yield produced by plants grown from seed for a control plant. Selection methods can be applied in multiple and diverse geographic locations, for example up to 16 or more locations, over one or more planting seasons, for example at least two planting seasons to statistically distinguish yield improvement from natural environmental effects. Each of the transgenic corn plants and soybean plants with a nucleus of the invention prepared in Examples 6 and 7 are screened for yield enhancement. At least one event from each of the corn plants is selected as having at least between 3 and 5% increase in yield as compared to a control plant as having a nucleus of this invention.

C. Selection for Enhanced Water Use Efficiency (WUE)

The following is a high-throughput method for screening for water use efficiency in a greenhouse to identify the transgenic corn plants with a nucleus of this invention. This selection process imposes 3 drought/re-water cycles on plants over a total period of 15 days after an initial stress free growth period of 11 days. Each cycle consists of 5 days, with no water being applied for the first four days and a water quenching on the 5th day of the cycle. The primary phenotypes analyzed by the selection method are the changes in plant growth rate as determined by height and biomass during a vegetative drought treatment. The hydration status of the shoot tissues following the drought is also measured. The plant heights are measured at three time points. The first is taken just prior to the onset drought when the plant is 11 days old, which is the shoot initial height (SIH). The plant height is also measured halfway throughout the drought/re-water regimen, on day 18 after planting, to give rise to the shoot mid-drought height (SMH). Upon the completion of the final drought cycle on day 26 after planting, the shoot portion of the plant is harvested and measured for a final height, which is the shoot wilt height (SWH) and also measured for shoot wilted biomass (SWM). The shoot is placed in water at 40 degree Celsius in the dark. Three days later, the shoot is weighted to give rise to the shoot turgid weight (STM). After drying in an oven for four days, the shoots are weighted for shoot dry biomass (SDM). The shoot average height (SAH) is the mean plant height across the 3 height measurements. The procedure described above can be adjusted for +/−˜one day for each step given the situation.

To correct for slight differences between plants, a size corrected growth value is derived from STH and SWH. This is the Relative Growth Rate (RGR). Relative Growth Rate (RGR) is calculated for each shoot using the formula [RGR %=(SWH−SIH)/((SWH+SIH)/2)×100]. Relative water content (RWC) is a measurement of how much (%) of the plant was water at harvest. Water Content (RWC) is calculated for each shoot using the formula [RWC %=(SWM−SDM)/(STM−SDM)×100]. Fully watered corn plants of this age run around 98% RWC.

Transgenic corn plants and soybean plants prepared in Examples 6 and 7 are screened for water use efficiency. Transgenic plants having at least a 1% increase in RGR and RWC as compared to control plants are identified as having enhanced water used efficiency and are selected as having a nucleus of this invention. Transgenic corn and soybean plants having in their nucleus DNA identified in Table 3 as imparting drought tolerance enhancement (DS, HS, SS, and PEG) and homologous DNA are identified as showing increased water use efficiency as compared to control plants and are selected as having a nucleus of this invention.

D. Selection for Growth Under Cold Stress

Cold germination assay—Three sets of seeds are used for the assay. The first set consists of positive transgenic events (F 1 hybrid) where the genes of the present invention are expressed in the seed. The second seed set is nontransgenic, wild-type negative control made from the same genotype as the transgenic events. The third set consisted of two cold tolerant and one cold sensitive commercial check lines of corn. All seeds are treated with a fungicide “Captan” (MAESTRO® 80DF Fungicide, Arvesta Corporation, San Francisco, Calif., USA). 0.43 mL Captan is applied per 45 g of corn seeds by mixing it well and drying the fungicide prior to the demonstration.

Corn kernels are placed embryo side down on blotter paper within an individual cell (8.9×8.9 cm) of a germination tray (54×36 cm). Ten seeds from an event are placed into one cell of the germination tray. Each tray can hold 21 transgenic events and 3 replicates of wildtype (LH244SDms+LH59), which is randomized in a complete block design. For every event there are five replications (five trays). The trays are placed at 9.7 C for 24 days (no light) in a Convrion® growth chamber (Conviron Model PGV36, Controlled Environments, Winnipeg, Canada). Two hundred and fifty millilters of deionized water are added to each germination tray. Germination counts are taken 10th, 11th, 12th, 13th, 14th, 17th, 19th, 21st, and 24th day after start date of the demonstration. Seeds are considered germinated if the emerged radical size is 1 cm. From the germination counts germination index is calculated.

The germination index is calculated as per:

Germination index=(Σ([T+1−n_(i)]*[P_(i)−P_(i-1)]))/T where T is the total number of days for which the germination assay is performed. The number of days after planting is defined by n. “i” indicated the number of times the germination had been counted, including the current day. P is the percentage of seeds germinated during any given rating. Statistical differences are calculated between transgenic events and wild type control. After statistical analysis, the events that show a statistical significance at the p level of less than 0.1 relative to wild-type controls will advance to a secondary cold selection. The secondary cold screen is conducted in the same manner of the primary selection only increasing the number of repetitions to ten. Statistical analysis of the data from the secondary selection is conducted to identify the events that show a statistical significance at the p level of less than 0.05 relative to wild-type controls.

Transgenic corn plants and soybean plants prepared in Examples 6 and 7 are screened for water use efficiency. Transgenic plants having at least a 5% increase in germination index as compared to control plants are identified as having enhanced cold stress tolerance and are selected as having a nucleus of this invention. Transgenic corn and soybean plants having in their nucleus DNA identified in Table 3 as imparting cold tolerance enhancement (CK or CS) and homologous DNA are identified as showing increased cold stress tolerance as compared to control plants and are selected as having a nucleus of this invention.

E. Screens for Transgenic Plant Seeds with Increased Protein and/or Oil Levels

The following is a high-throughput selection method for identifying plant seeds with improvement in seed composition using the Infratec® 1200 series Grain Analyzer, which is a near-infrared transmittance spectrometer used to determine the composition of a bulk seed sample. Near infrared analysis is a non-destructive, high-throughput method that can analyze multiple traits in a single sample scan. An NIR calibration for the analytes of interest is used to predict the values of an unknown sample. The NIR spectrum is obtained for the sample and compared to the calibration using a complex chemometric software package that provides a predicted values as well as information on how well the sample fits in the calibration.

Infratec® Model 1221, 1225, or 1227 analyzer with transport module by Foss North America is used with cuvette, item #1000-4033, Foss North America or for small samples with small cell cuvette, Foss standard cuvette modified by Leon Girard Co. Corn and soy check samples of varying composition maintained in check cell cuvettes are supplied by Leon Girard Co. NIT collection software is provided by Maximum Consulting Inc. Calculations are performed automatically by the software. Seed samples are received in packets or containers with barcode labels from the customer. The seed is poured into the cuvettes and analyzed as received.

TABLE 23 Typical sample(s): Whole grain corn and soybean seeds Analytical time to Less than 0.75 min per sample run method: Total elapsed time 1.5 minute per sample per run: Typical and minimum Corn typical: 50 cc; minimum 30 cc sample size: Soybean typical: 50 cc; minimum 5 cc Typical analytical Determined in part by the specific range: calibration. Corn - moisture 5-15%, oil 5-20%, protein 5-30%, starch 50-75%, and density 1.0-1.3%. Soybean - moisture 5-15%, oil 15-25%, and protein 35-50%.

Transgenic corn plants and soybean plants prepared in Examples 6 and 7 are screened for increased protein and oil in seed. Transgenic inbred corn and soybean plants having an increase of at least 1 percentage point in the total percent seed protein or at least 0.3 percentage point in total seed oil and transgenic hybrid corn plants having an increase of at least 0.4 percentage point in the total percent seed protein as compared to control plants are identified as having enhanced seed protein or enhanced seed oil and are selected as having a nucleus of this invention.

Example 9 Cotton Transgenic Plants with Enhanced Agronomic Traits

Cotton transformation is performed as generally described in WO0036911 and in U.S. Pat. No. 5,846,797 and are incorporated herein by reference. Transgenic cotton plants containing each of the recombinant DNA having a sequence of SEQ ID NO: 1 through SEQ ID NO: 139 are obtained by transforming with recombinant DNA from each of the genes identified in Table 1. Progeny transgenic plants are selected from a population of transgenic cotton events under specified growing conditions and are compared with control cotton plants. Control cotton plants are substantially the same cotton genotype but without the recombinant DNA, for example, either a parental cotton plant of the same genotype that was not transformed with the identical recombinant DNA or a negative isoline of the transformed plant. Additionally, a commercial cotton cultivar adapted to the geographical region and cultivation conditions, i.e. cotton variety ST474, cotton variety FM 958, and cotton variety Siokra L-23, are used to compare the relative performance of the transgenic cotton plants containing the recombinant DNA. The specified culture conditions are growing a first set of transgenic and control plants under “wet” conditions, e.g., irrigated in the range of 85 to 100 percent of evapotranspiration to provide leaf water potential of −14 to −18 bars, and growing a second set of transgenic and control plants under “dry” conditions, e.g., irrigated in the range of 40 to 60 percent of evapotranspiration to provide a leaf water potential of −21 to −25 bars. Pest control, such as weed and insect control is applied equally to both wet and dry treatments as needed. Data gathered during the trial includes weather records throughout the growing season including detailed records of rainfall; soil characterization information; any herbicide or insecticide applications: any gross agronomic differences observed such as leaf morphology, branching habit, leaf color, time to flowering, and fruiting pattern; plant height at various points during the trial; stand density; node and fruit number including node above white flower and node above crack boll measurements; and visual wilt scoring. Cotton boll samples are taken and analyzed for lint fraction and fiber quality. The cotton is harvested at the normal harvest timeframe for the trial area. Enhanced water use efficiency is indicated by increased yield, improved relative water content, enhanced leaf water potential, increased biomass, enhanced leaf extension rates, and improved fiber parameters.

The transgenic cotton plants of this invention are identified from among the transgenic cotton plants by agronomic trait screening as having increased yield and enhanced water use efficiency.

Example 10 Canola Plants with Enhanced Agrominic Traits

This example illustrates plant transformation useful in producing the transgenic canola plants of this invention and the production and identification of transgenic seed for transgenic canola having enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.

Tissues from in vitro grown canola seedlings are prepared and inoculated with a suspension of overnight grown Agrobacterium containing plasmid DNA with the gene of interest cassette and a plant selectable marker cassette. Following co-cultivation with Agrobacterium, the infected tissues are allowed to grow on selection to promote growth of transgenic shoots, followed by growth of roots from the transgenic shoots. The selected plantlets are then transferred to the greenhouse and potted in soil. Molecular characterizations are performed to confirm the presence of the gene of interest, and its expression in transgenic plants and progenies. Progeny transgenic plants are selected from a population of transgenic canola events under specified growing conditions and are compared with control canola plants. Control canola plants are substantially the same canola genotype but without the recombinant DNA, for example, either a parental canola plant of the same genotype that is not transformed with the identical recombinant DNA or a negative isoline of the transformed plant

Transgenic canola plant cells are transformed with recombinant DNA from each of the genes identified in Table 2. Transgenic progeny plants and seed of the transformed plant cells are screened for enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.

Example 11 Monocot and Dicot Plant Transformation for the Suppression of Endogeneous Protein

This example illustrates monocot and dicot plant transformation to produce nuclei of this invention in cells of a transgenic plant by transformation where the recombinant DNA suppresses the expression of an endogenous protein identified in Table 24.

Corn, soybean, cotton, or canola tissue are transformed as describe in Examples 6, 7, 9 or 10 using recombinant DNA in the nucleus with DNA that transcribes to RNA that forms double-stranded RNA targeted to an endogenous gene with DNA encoding the protein. The genes for which the double-stranded RNAs are targeted are the native gene in corn and soybean that are homolog of the genes encoding the protein of Arabidopsis thaliana as identified in table 24.

Populations of transgenic plants prepared in Examples 5, 6, 7, 9 or 10 with DNA for suppressing a gene identified in Table 2 as providing an enhanced trait by gene suppression are screened to identify an event from those plants with a nucleus of the invention by selecting the trait identified in this specification.

TABLE 24 PEP SEQ ID Pfam module Construct ID Traits 142 RWP-RK 70733 SP 144 AUX_IAA 15707 SS 151 SRF-TF 10106 LN 197 zf-C3HC4 10456 LL 198 Myb_DNA-binding 11115 PEG 206 CCT 10362 HS 250 PHD 12179 HS 273 EIN3 10114 SS 275 AP2 10804 LN 

What is claimed is:
 1. A plant cell nucleus with stably-integrated, recombinant DNA comprising a promoter that is functional in plant cells and that is operably linked to protein coding DNA encoding a protein having an amino acid sequence comprising a Pfam domain module Linker_histone::AT_hook::AT_hook::AT_hook::AT_hook; wherein said plant cell nucleus is selected by screening a population of transgenic plants that have said recombinant DNA in its nuclei and express said protein for an enhanced trait as compared to control plants that do not have said recombinant DNA in their nuclei; and wherein said enhanced trait is selected from group of enhanced traits consisting of enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.
 2. A plant cell nucleus with stably integrated, recombinant DNA, wherein a. said recombinant DNA comprises a promoter that is functional in said plant cell and that is operably linked to a protein coding DNA encoding a protein having an amino acid sequence comprising a Pfam domain module selected from the group consisting of WRKY::WRKY, AP2, AUX_IAA, WRKY, WRKY, HLH, Myb_DNA-binding::Linker_histone, zf-B_box::zf-B_box, Ank::Ank::Ank::Chromo, NAM, zf-C2H2, Myb_DNA-binding, bZIP_I, PHD, Linker_histone::AT_hook::AT_hook::AT_hook::AT_hook, B3::Auxin_resp, HLH, zf-Dof, AT_hook::DUF296, AT_hook::AT_hook::DUF296, NAM, GATA, NAM, Myb_DNA-binding, zf-B_box::CCT, POX::Homcobox, B3::Auxin_resp::AUX_IAA, Myb_DNA-binding::Myb_DNA-binding, Myb_DNA-binding::Myb_DNA-binding, zf-C2H2, zf-C2H2, Myb_DNA-binding::Myb_DNA-binding, Myb_DNA-binding::Myb_DNA-binding, TCP, KNOX1::KNOX2, zf-ZPRJ::zf-ZPR1, Myb_DNA-binding::Myb_DNA-binding, DUF630::DUF632, WRKY, Myb_DNA-binding, zf-C2H2, HLH, AP2, AT_hook::DUF296, Ank::Ank::Ank::Ank::Ank, WRKY, zf-C2H2, NAM, AP2, NAM, Myb_DNA-binding::Myb_DNA-binding::Myb_DNA-binding, NAM, HLH, Myb_DNA-binding::Myb_DNA-binding Myb_DNA-binding, HLH, bZIP_2, bZIP_2, BAH::PHD, HLH, NAM, GATA, SSrecog::Rtt106::HMG_box, DUF573, zf-B_box::CCT, HLH, RWP-RK, AP2::B3, AUX_IAA, SRF-TF, AP2, AP2, HSF_DNA-bind, AP2, SRF-TF::K-box, Myb_DNA-binding, zf-LSD1::zf-LSD1::zf-LSD1, KNOX1::KNOX2::ELK, zf-C3HC4, MFMR::bZIP_1, DUF573, Myb_DNA-binding, HLH, NAM, Myb_DNA-binding::Myb_DNA-binding, SRF-TF::K-box, zf-C3HC4, zf-B_box, WRKY, zf-B_box::CCT, EIN3, HSF_DNA-bind, AUX_LAA, TCP, Myb_DNA-binding::Myb_DNA-binding, AP2, KNOX1::KNOX2::ELK::Homeobox, HSF_DNA-bind, HSF_DNA-bind, AP2::B3, NAM, SBP, AP2, zf-C2H2, SRF-TF::K-box, zf-C2H2, GRAS, AP2, Myb_DNA-binding, AP2, AP2::AP2, HLH, CXC::CXC, AP2, NAM, zf-C3HC4, Myb_DNA-binding::Myb_DNA-binding, GRAS, Homeobox::HALZ, Myb_DNA-binding, NAM, WRKY, zf-C2H2, zf-C2H2, NAM, zf-C2H2, AP2::AP2, zf-C3HC4, RWP-RK::PB1, SRF-TF::K-box, and zf-B_box; b. said recombinant DNA comprises a promoter that is functional in said plant cell and that is operably linked to a protein coding DNA encoding a protein comprising an amino acid sequence with at least 90% identity to a consensus amino acid sequence selected from the group consisting of SEQ ID NO: 6027 through 6034; or c. said recombinant DNA suppresses comprises a promoter that is functional in said plant cell and operably linked to DNA that transcribe into RNA that suppresses the level of an endogenous protein wherein said endogenous protein has an amino acid sequence comprising a pfam domain module selected from the group consisting of RWP-RK, AUX_IAA, SRF-TF, zf-C3HC4, Myb_DNA-binding, CCT, PHD, EIN3, and AP2; and wherein said plant cell nucleus is selected by screening a population of transgenic plants that have said recombinant DNA and an enhanced trait as compared to control plants that do not have said recombinant DNA in their nuclei; and wherein said enhanced trait is selected from group of enhanced traits consisting of enhanced water use efficiency, enhanced cold tolerance, enhanced heat tolerance, enhanced resistance to salt exposure, enhanced shade tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.
 3. The plant cell nucleus of claim 2 wherein said protein coding DNA encodes a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 140 through SEQ ID NO:
 6023. 4. The plant cell nucleus of claim 2 further comprising DNA expressing a protein that provides tolerance from exposure to an herbicide applied at levels that are lethal to a wild type of said plant cell.
 5. The plant cell nucleus of claim 4 wherein said herbicide is a glyphosate, dicamba, or glufosinate compound.
 6. A transgenic plant cell or plant comprising a plurality of plant cells with the plant cell nucleus of claim
 2. 7. The transgenic plant cell or plant of claim 6 which is homozygous for said recombinant DNA.
 8. A transgenic seed comprising a plurality of plant cells with a plant cell nucleus of claim
 2. 9. The transgenic seed of claim 8 from a corn, soybean, cotton, canola, alfalfa, wheat or rice plant.
 10. A transgenic pollen grain comprising a haploid derivative of a plant cell nucleus of claim
 2. 11. A method for manufacturing non-natural, transgenic seed that can be used to produce a crop of transgenic plants with an enhanced trait resulting from expression of recombinant DNA in a nucleus of claim 2, wherein said method for manufacturing said transgenic seed comprising: (a) screening a population of plants for said enhanced trait and said recombinant DNA, wherein individual plants in said population can exhibit said trait at a level less than, essentially the same as or greater than the level that said trait is exhibited in control plants which do not contain the recombinant DNA, wherein said enhanced trait is selected from the group of enhanced traits consisting of enhanced water use efficiency, enhanced cold tolerance, enhanced heat tolerance, enhanced high salinity tolerance, enhanced shade tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil, (b) selecting from said population one or more plants that exhibit said trait at a level greater than the level that said trait is exhibited in control plants, and (c) collecting seeds from selected plant selected from step b.
 12. The method of claim 11 wherein said method for manufacturing said transgenic seed further comprising (a) verifying that said recombinant DNA is stably integrated in said selected plants, and (b) analyzing tissue of said selected plant to determine the expression or suppression of a protein having the function of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 140-278.
 13. The method of claim 11 wherein said seed is corn, soybean, cotton, alfalfa, canola wheat or rice seed.
 14. A method of producing hybrid corn seed comprising: (a) acquiring hybrid corn seed from a herbicide tolerant corn plant which also has stably-integrated, recombinant DNA in a nucleus of claim 2; (b) producing corn plants from said hybrid corn seed, wherein a fraction of the plants produced from said hybrid corn seed is homozygous for said recombinant DNA, a fraction of the plants produced from said hybrid corn seed is hemizygous for said recombinant DNA, and a fraction of the plants produced from said hybrid corn seed has none of said recombinant DNA; (c) selecting corn plants which are homozygous and hemizygous for said recombinant DNA by treating with an herbicide; (d) collecting seed from herbicide-treated-surviving corn plants and planting said seed to produce further progeny corn plants; (e) repeating steps (c) and (d) at least once to produce an inbred corn line; and (f) crossing said inbred corn line with a second corn line to produce hybrid seed.
 15. A transgenic plant comprising recombinant DNA constructs encoding amino acid sequence that have at least 90% identity over at least 90% of the length of a reference sequence selected from the group consisting of SEQ ID NOs: 140-278 when the amino acid sequence is aligned to the reference sequence. 